Pierrick Roger
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 686a27c |
| git_last_commit_date: 2024-10-29 11:04:36 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:14 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 200/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbChebi_1.13.0.tar.gz |
| StartedAt: 2024-11-27 20:36:07 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 20:41:41 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 333.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-11-27 20:40:28.749][biodb::testContext]
biodb.INFO [2024-11-27 20:40:28.750][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:40:28.751][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-11-27 20:40:28.752][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:40:28.753][biodb::testContext]
biodb.INFO [2024-11-27 20:40:28.758][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:40:28.760][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-27 20:40:28.766][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:40:28.767][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-27 20:40:28.768][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-27 20:40:28.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.771][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-27 20:40:28.789][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-27 20:40:28.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.793][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-27 20:40:28.794][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-27 20:40:28.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.797][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-27 20:40:28.798][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-27 20:40:28.799][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-27 20:40:28.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.802][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-27 20:40:28.803][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-27 20:40:28.804][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-27 20:40:28.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.808][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-27 20:40:28.809][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-27 20:40:28.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.812][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-27 20:40:28.813][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-27 20:40:28.814][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-27 20:40:28.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.817][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-27 20:40:28.818][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-27 20:40:28.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.820][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[2024-11-27 20:40:28.821][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-27 20:40:28.822][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-27 20:40:28.823][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-27 20:40:28.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.826][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:40:28.827][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-27 20:40:28.828][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-27 20:40:28.829][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-27 20:40:28.830][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-27 20:40:28.831][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-27 20:40:28.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.834][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-27 20:40:28.835][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-27 20:40:28.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.839][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-27 20:40:28.840][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-27 20:40:28.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.843][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-27 20:40:28.844][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-27 20:40:28.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.847][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-27 20:40:28.848][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-27 20:40:28.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.851][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.DEBUG[2024-11-27 20:40:28.852][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-27 20:40:28.853][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-27 20:40:28.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.856][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:40:28.857][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-27 20:40:28.862][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-27 20:40:28.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.865][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-27 20:40:28.866][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-27 20:40:28.867][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-27 20:40:28.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:28.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:28.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:28.873][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-27 20:40:28.902][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:28.923][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-27 20:40:28.924][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.925][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:40:28.925][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.926][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.927][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:28.928][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.929][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:40:28.930][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:40:28.931][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.932][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-27 20:40:28.933][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:40:28.934][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.934][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.935][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:40:28.935][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:40:28.935][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:40:28.935][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:40:28.935][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:40:28.936][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:40:28.937][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:28.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:28.939][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:40:28.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:28.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:28.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.942][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.943][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:40:28.944][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:40:28.945][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:28.946][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.947][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-27 20:40:28.949][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:28.950][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:40:28.950][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.951][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:40:28.952][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.953][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.954][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:28.955][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.956][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:40:28.957][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:40:28.958][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.959][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-27 20:40:28.960][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:40:28.961][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.961][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.962][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:40:28.962][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:40:28.962][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:40:28.962][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:40:28.962][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:40:28.963][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:40:28.964][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:28.965][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:28.966][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:40:28.967][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:28.968][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:28.969][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.970][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.970][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:40:28.971][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:40:28.972][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:28.973][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.974][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-27 20:40:28.976][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.977][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-27 20:40:28.978][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.979][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:40:28.980][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.981][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:28.982][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.983][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:40:28.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:40:28.985][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:28.986][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-27 20:40:28.987][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:40:28.988][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.989][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:28.990][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.990][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:40:28.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:28.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:28.993][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:40:28.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:28.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:28.996][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:40:28.997][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:28.997][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:40:28.998][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:40:28.999][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:29.000][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:29.001][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-27 20:40:29.003][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.004][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:40:29.005][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.006][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:40:29.006][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.007][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:40:29.008][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:29.009][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:40:29.010][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:40:29.011][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:40:29.012][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:29.013][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-27 20:40:29.014][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:40:29.015][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:29.016][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.016][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:29.017][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:40:29.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:29.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:29.020][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:40:29.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:29.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:29.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:40:29.024][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:29.024][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:40:29.025][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:40:29.026][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:29.027][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:40:29.030][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:40:29.031][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.057][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[2024-11-27 20:40:29.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.073][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[2024-11-27 20:40:29.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.098][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[2024-11-27 20:40:29.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.107][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-27 20:40:29.111][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-27 20:40:29.112][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-27 20:40:29.114][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-27 20:40:29.116][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:40:29.118][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-27 20:40:29.120][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-27 20:40:29.121][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-27 20:40:29.122][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-27 20:40:29.123][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-27 20:40:29.125][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:40:29.126][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-27 20:40:29.127][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-27 20:40:29.129][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-27 20:40:29.130][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-27 20:40:29.131][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-27 20:40:29.132][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-27 20:40:29.134][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-27 20:40:29.135][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:40:29.136][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-27 20:40:29.137][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-27 20:40:29.139][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-27 20:40:29.140][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-27 20:40:29.141][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-27 20:40:29.143][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-27 20:40:29.144][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-27 20:40:29.151][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-27 20:40:29.154][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-27 20:40:29.155][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-27 20:40:29.157][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-27 20:40:29.158][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-27 20:40:29.159][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-27 20:40:29.161][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-27 20:40:29.162][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-27 20:40:29.164][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-27 20:40:29.165][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-27 20:40:29.167][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-27 20:40:29.168][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-27 20:40:29.169][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-27 20:40:29.171][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-27 20:40:29.172][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-27 20:40:29.174][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-27 20:40:29.175][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-27 20:40:29.177][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-27 20:40:29.178][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-27 20:40:29.180][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-27 20:40:29.181][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-27 20:40:29.183][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-27 20:40:29.184][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-27 20:40:29.185][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-27 20:40:29.187][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-27 20:40:29.188][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-27 20:40:29.190][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-27 20:40:29.191][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-27 20:40:29.193][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-27 20:40:29.194][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-27 20:40:29.196][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-27 20:40:29.197][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-27 20:40:29.198][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-27 20:40:29.200][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-27 20:40:29.201][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-27 20:40:29.203][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-27 20:40:29.204][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-27 20:40:29.206][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-27 20:40:29.207][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-27 20:40:29.208][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-27 20:40:29.210][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:40:29.211][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:40:29.213][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-27 20:40:29.214][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-27 20:40:29.216][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-27 20:40:29.217][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-27 20:40:29.218][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-27 20:40:29.220][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-27 20:40:29.221][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-27 20:40:29.223][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-27 20:40:29.224][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-27 20:40:29.225][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-27 20:40:29.227][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-27 20:40:29.228][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-27 20:40:29.230][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-27 20:40:29.231][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-27 20:40:29.232][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-27 20:40:29.239][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-27 20:40:29.241][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:40:29.245][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:40:29.246][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.247][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.259][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[2024-11-27 20:40:29.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.297][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[2024-11-27 20:40:29.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.310][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.DEBUG[2024-11-27 20:40:29.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:40:29.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:29.371][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-27 20:40:29.380][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-27 20:40:29.382][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:29.383][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-27 20:40:29.384][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.385][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:40:29.385][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.386][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:40:29.387][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.388][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-27 20:40:29.389][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-27 20:40:29.390][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:40:29.391][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.392][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-27 20:40:29.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-27 20:40:29.394][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-27 20:40:29.395][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-27 20:40:29.396][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:40:29.396][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:40:29.396][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:40:29.397][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-27 20:40:29.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:29.398][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:29.399][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:40:29.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:40:29.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:40:29.402][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:40:29.403][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:29.403][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-27 20:40:29.404][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:40:29.405][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:40:29.405][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-27 20:40:29.406][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-27 20:40:29.406][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-27 20:40:29.412][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:40:29.413][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:40:29.415][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-27 20:40:29.416][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:40:29.418][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:40:29.419][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:40:29.443][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-27 20:40:29.445][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-27 20:40:29.449][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-27 20:40:29.454][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-27 20:40:29.458][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:40:29.459][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:40:29.469][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-27 20:40:29.470][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-27 20:40:29.478][biodb::testThat]
biodb.INFO [2024-11-27 20:40:29.479][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-11-27 20:40:29.480][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:29.481][biodb::testThat]
biodb.TRACE[2024-11-27 20:40:29.485][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-11-27 20:40:29.487][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:29.490][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:29.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:29.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:29.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:29.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:29.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:29.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:29.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:29.525][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.526][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.528][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.546][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:29.548][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:29.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.549][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.577][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:29.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:29.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.581][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:29.583][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:29.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.585][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.586][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:29.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:29.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.590][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:29.591][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:29.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.593][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:29.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:29.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.599][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:29.600][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:29.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.602][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:29.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:29.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.607][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:29.609][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:29.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.611][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.612][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:29.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:29.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.616][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:29.617][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:29.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.619][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:29.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.625][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:29.626][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:29.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.628][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:29.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:29.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.633][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:29.634][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:29.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.690][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:29.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:29.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.695][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:29.696][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:29.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.698][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.699][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:29.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:29.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.703][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:29.704][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:29.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.706][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.707][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:29.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:29.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:29.784][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-11-27 20:40:29.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:29.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:29.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:29.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:29.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:29.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:29.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:29.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:29.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:29.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:29.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.839][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:40:29.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:40:29.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.843][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:40:29.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:40:29.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-27 20:40:29.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-27 20:40:29.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.851][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-27 20:40:29.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-27 20:40:29.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.954][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.955][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.956][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:29.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:29.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.987][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.988][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.990][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:29.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:29.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:29.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.014][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.015][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.017][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.030][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:30.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:30.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:30.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:30.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.037][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:30.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:30.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.041][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:30.042][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:30.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.044][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.045][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:30.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:30.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.068][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.069][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.071][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.095][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.096][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.098][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.110][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:30.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:30.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.119][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:30.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:30.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.123][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:30.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:30.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.127][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:30.128][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:30.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.130][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.131][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:30.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:30.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.142][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.146][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.150][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.154][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.155][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.156][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.157][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.168][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.172][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.176][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.180][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.181][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.183][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.184][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.195][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:30.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:30.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.199][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:30.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:30.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.203][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:30.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:30.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.207][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:30.208][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:30.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.210][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:30.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:30.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.234][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.235][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.237][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.267][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.269][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.281][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.282][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.284][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.288][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:30.289][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:30.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.291][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.295][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:30.296][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:30.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.298][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.302][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.303][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.305][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.309][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.310][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.312][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.316][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.317][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.324][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.325][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.327][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.331][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.332][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.334][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.338][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.339][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.341][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.345][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.346][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.348][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.352][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:30.353][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:30.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.355][ef$get] fields variable is a list.
biodb.INFO [2024-11-27 20:40:30.362][biodb::testThat]
biodb.INFO [2024-11-27 20:40:30.363][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-27 20:40:30.364][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:30.365][biodb::testThat]
biodb.DEBUG[2024-11-27 20:40:30.378][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-11-27 20:40:30.385][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:30.389][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-11-27 20:40:30.390][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:30.392][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-11-27 20:40:30.393][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:30.423][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:30.424][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:30.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:30.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:30.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:30.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:30.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:30.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:30.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:30.438][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.439][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.441][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.463][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:30.464][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:30.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.466][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.467][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:30.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:30.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.471][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:30.472][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:30.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.474][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.476][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:30.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:30.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.480][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.481][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.483][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.488][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.489][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.491][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.496][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.497][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.499][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.500][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:30.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.504][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:30.505][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.507][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.508][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:30.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.513][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.515][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.521][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.522][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.523][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.529][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:30.530][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.537][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.538][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:30.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:30.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.542][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:30.543][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:30.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.545][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.546][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:30.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:30.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:30.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:30.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:30.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:30.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:30.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:30.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:30.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:30.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:30.590][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-11-27 20:40:30.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-27 20:40:30.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-27 20:40:30.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-27 20:40:30.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-27 20:40:30.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-27 20:40:30.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-27 20:40:30.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:40:30.610][biodb::testThat]
biodb.INFO [2024-11-27 20:40:30.610][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-27 20:40:30.611][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:30.612][biodb::testThat]
biodb.TRACE[2024-11-27 20:40:30.615][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.616][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.618][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:30.620][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-11-27 20:40:30.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:30.659][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-11-27 20:40:30.663][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-27 20:40:30.690][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:30.706][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-27 20:40:30.707][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:30.709][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-27 20:40:30.731][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:30.735][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:30.736][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:40:30.737][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:30.739][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:40:30.741][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-11-27 20:40:30.752][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.753][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:30.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.755][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.756][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.757][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.759][ef$get] fields variable is a list.
biodb.INFO [2024-11-27 20:40:30.763][biodb::testThat]
biodb.INFO [2024-11-27 20:40:30.764][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-11-27 20:40:30.765][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:30.766][biodb::testThat]
biodb.TRACE[2024-11-27 20:40:30.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:30.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:30.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:30.862][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:30.865][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:30.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:40:30.868][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:30.870][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-11-27 20:40:30.885][biodb::testThat]
biodb.INFO [2024-11-27 20:40:30.886][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-11-27 20:40:30.888][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:30.889][biodb::testThat]
biodb.TRACE[2024-11-27 20:40:30.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.917][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.939][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:40:30.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:40:30.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.943][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:40:30.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:40:30.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-27 20:40:30.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-27 20:40:30.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.951][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-27 20:40:30.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-27 20:40:30.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:30.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:30.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:30.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:30.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:30.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:30.997][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:40:30.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:40:30.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:31.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:31.001][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:40:31.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:40:31.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:31.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:31.005][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-27 20:40:31.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-27 20:40:31.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:31.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:31.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-27 20:40:31.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-27 20:40:31.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:31.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:40:31.018][biodb::testThat]
biodb.INFO [2024-11-27 20:40:31.019][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-27 20:40:31.020][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:31.021][biodb::testThat]
biodb.INFO [2024-11-27 20:40:31.029][biodb::testThat]
biodb.INFO [2024-11-27 20:40:31.030][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-27 20:40:31.031][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:31.032][biodb::testThat]
biodb.INFO [2024-11-27 20:40:31.040][biodb::testThat]
biodb.INFO [2024-11-27 20:40:31.041][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-27 20:40:31.042][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:31.043][biodb::testThat]
biodb.DEBUG[2024-11-27 20:40:31.047][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-11-27 20:40:32.134][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-11-27 20:40:33.433][biodb::testThat]
biodb.INFO [2024-11-27 20:40:33.434][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-27 20:40:33.435][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:33.436][biodb::testThat]
biodb.DEBUG[2024-11-27 20:40:33.860][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-11-27 20:40:34.296][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:34.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:34.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.354][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:34.355][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:34.356][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:34.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.359][ef$get] fields variable is a list.
biodb.INFO [2024-11-27 20:40:34.361][biodb::testThat]
biodb.INFO [2024-11-27 20:40:34.362][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-11-27 20:40:34.363][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:40:34.364][biodb::testThat]
biodb.TRACE[2024-11-27 20:40:34.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:34.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:34.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:34.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:34.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:34.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:34.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:34.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:34.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:34.468][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:34.471][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:34.472][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:40:34.473][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:34.475][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:40:34.532][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:34.535][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:34.536][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:40:34.537][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:34.539][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-11-27 20:40:34.555][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-27 20:40:34.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-27 20:40:34.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:34.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:34.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:34.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:34.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:34.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:34.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:34.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:34.588][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:34.591][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:34.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-27 20:40:34.593][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:34.595][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-27 20:40:34.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:34.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:34.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:34.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:34.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:34.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:34.606][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[2024-11-27 20:40:34.607][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-11-27 20:40:34.656][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:34.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-11-27 20:40:34.659][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:34.660][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:34.661][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:34.662][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:34.663][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:34.664][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:34.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:34.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:34.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:34.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:34.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:34.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:34.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:34.676][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-11-27 20:40:34.679][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:34.680][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:34.681][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-11-27 20:40:35.024][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-11-27 20:40:35.374][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:35.376][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-11-27 20:40:35.408][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-11-27 20:40:35.412][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-11-27 20:40:35.415][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:35.417][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:35.419][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:35.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:35.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:35.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:35.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:35.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:35.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:35.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:35.437][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.438][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.440][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.456][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:35.457][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:35.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.459][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.460][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:35.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:35.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.464][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:35.465][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:35.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.467][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.468][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:35.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.473][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:35.474][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:35.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.476][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:35.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:35.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.481][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:35.482][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:35.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.484][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:35.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:35.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.489][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:35.490][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:35.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.492][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.493][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:35.495][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.496][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.498][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:35.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.502][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:35.503][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:35.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.505][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:35.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:35.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.510][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:35.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:35.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.513][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:35.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:35.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.518][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:35.519][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:35.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.521][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.522][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:35.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:35.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.526][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:35.527][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:35.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.529][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.531][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:35.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:35.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:35.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:35.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:35.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:35.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:35.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:35.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:35.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:35.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:35.580][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-11-27 20:40:35.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:35.603][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:35.606][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:35.608][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-27 20:40:35.609][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:35.610][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-27 20:40:35.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:35.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:35.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:35.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:35.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:35.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:35.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:35.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:35.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:35.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:35.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:35.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:35.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:35.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:35.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:35.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:35.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:35.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:35.664][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-11-27 20:40:35.665][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:35.667][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-11-27 20:40:35.668][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:35.669][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:35.670][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:35.672][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:35.673][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:35.673][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:35.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:35.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:35.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:35.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:35.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:35.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:35.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:35.699][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-11-27 20:40:35.715][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:35.716][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:35.736][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-11-27 20:40:36.078][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-11-27 20:40:36.428][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:36.432][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-11-27 20:40:36.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-11-27 20:40:36.446][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-11-27 20:40:36.449][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:36.452][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:36.454][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:36.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:36.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:36.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:36.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:36.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:36.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:36.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:36.480][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.482][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.485][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.492][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:36.494][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:36.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.496][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.498][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:36.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:36.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.503][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:36.504][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:36.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.506][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:36.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:36.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.512][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:36.514][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:36.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.516][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:36.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:36.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.521][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:36.522][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:36.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.524][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:36.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:36.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.529][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:36.530][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:36.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.532][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.533][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:36.534][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.536][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.537][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:36.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.541][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:36.542][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:36.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.544][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:36.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:36.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.559][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:36.560][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:36.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.561][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:36.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:36.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.567][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:36.568][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:36.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.570][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.571][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:36.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:36.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.575][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:36.576][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:36.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.578][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.580][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:36.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:36.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:36.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:36.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:36.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:36.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:36.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:36.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:36.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:36.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:36.624][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-11-27 20:40:36.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:36.660][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:36.663][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:36.664][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:40:36.665][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:36.667][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:40:36.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:36.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:36.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:36.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:36.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:36.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:36.680][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.TRACE[2024-11-27 20:40:36.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:36.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:36.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:36.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:36.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:36.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:36.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:36.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:36.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:36.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:36.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:36.702][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-11-27 20:40:36.703][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:36.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-11-27 20:40:36.706][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:36.707][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:36.708][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:36.709][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:36.710][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:36.711][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:36.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:36.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:36.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:36.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:36.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:36.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:36.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:36.724][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-11-27 20:40:36.727][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:36.727][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:36.729][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-11-27 20:40:37.087][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-11-27 20:40:37.429][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:37.432][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-11-27 20:40:37.438][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-11-27 20:40:37.443][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-11-27 20:40:37.445][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:37.447][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:37.449][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:37.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:37.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:37.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:37.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:37.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:37.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:37.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:37.505][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.506][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.508][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.513][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:37.514][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:37.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.516][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.517][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:37.518][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:37.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.521][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:37.522][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:37.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.524][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.525][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:37.526][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:37.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.528][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.529][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:37.530][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:37.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.532][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.533][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:37.534][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.536][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.537][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:37.538][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:37.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.540][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.541][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:37.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:37.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.544][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:37.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:37.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.549][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:37.550][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:37.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.552][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.553][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:37.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:37.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.557][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:37.558][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:37.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.560][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:37.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:37.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:37.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:37.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:37.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:37.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:37.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:37.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:37.604][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-11-27 20:40:37.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:37.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:37.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:37.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:37.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:37.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:37.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:37.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:37.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:37.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:37.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:37.634][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-11-27 20:40:37.635][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:37.637][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-11-27 20:40:37.638][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:37.639][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:37.640][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:37.641][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:37.642][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:37.643][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:37.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:37.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:37.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:37.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:37.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:37.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:37.654][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[2024-11-27 20:40:37.655][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-11-27 20:40:37.658][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:37.659][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:37.660][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-11-27 20:40:38.002][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-11-27 20:40:38.352][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:38.355][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-11-27 20:40:38.358][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-11-27 20:40:38.361][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-11-27 20:40:38.362][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:38.363][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:38.365][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:38.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:38.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:38.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:38.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:38.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:38.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:38.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:38.389][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.390][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.392][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.398][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:38.399][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:38.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.401][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.402][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:38.403][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:38.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.405][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.407][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:38.408][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:38.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.410][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.411][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:38.412][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:38.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.414][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.415][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:38.416][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:38.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.418][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.419][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:38.420][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.422][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.423][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:38.424][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:38.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.426][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.427][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:38.429][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:38.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.430][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:38.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:38.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.436][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:38.437][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:38.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.439][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.440][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:38.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:38.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.444][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:38.446][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:38.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.447][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:38.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:38.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:38.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:38.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:38.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:38.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:38.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:38.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:38.495][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-11-27 20:40:38.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:38.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:38.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:38.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:38.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:38.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:38.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:38.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:38.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:38.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:38.526][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[2024-11-27 20:40:38.527][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-11-27 20:40:38.528][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:38.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-11-27 20:40:38.531][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:38.532][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:38.533][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:38.534][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:38.535][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:38.536][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:38.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:38.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:38.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:38.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:38.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:38.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:38.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:38.550][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-11-27 20:40:38.552][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:38.553][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:38.555][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-11-27 20:40:38.899][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-11-27 20:40:39.254][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:39.259][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-11-27 20:40:39.266][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-11-27 20:40:39.272][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-11-27 20:40:39.275][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:39.278][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:39.281][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:39.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:39.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:39.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:39.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:39.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:39.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:39.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:39.307][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.320][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.323][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.330][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:39.332][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:39.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.340][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.348][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:39.350][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:39.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.352][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.354][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:39.355][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:39.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.357][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.359][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:39.360][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:39.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.362][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.364][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:39.365][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:39.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.367][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.369][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:39.370][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.372][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.373][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:39.374][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:39.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.377][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.378][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:39.379][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:39.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.381][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:39.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:39.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.389][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:39.390][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:39.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.392][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.393][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:39.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:39.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.398][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:39.399][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:39.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.401][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:39.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:39.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:39.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:39.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:39.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:39.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:39.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:39.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:39.464][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-11-27 20:40:39.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:39.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:39.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:39.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:39.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:39.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:39.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:39.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:39.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:39.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:39.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:39.496][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-11-27 20:40:39.497][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:39.498][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-11-27 20:40:39.500][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:39.501][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:39.502][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:39.503][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:39.504][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:39.505][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:39.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:39.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:39.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:39.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:39.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:39.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:39.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:39.517][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-11-27 20:40:39.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:39.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:39.522][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-11-27 20:40:39.864][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-11-27 20:40:40.210][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:40.213][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-11-27 20:40:40.217][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-11-27 20:40:40.219][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-11-27 20:40:40.221][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:40.222][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:40.223][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:40.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:40.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:40.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:40.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:40.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:40.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:40.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:40.239][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.240][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.242][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.259][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:40.260][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:40.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.262][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.263][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:40.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:40.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.268][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:40.269][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:40.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.271][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:40.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:40.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.276][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:40.277][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:40.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.279][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:40.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:40.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.285][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:40.286][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:40.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.288][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:40.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:40.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.293][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:40.294][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:40.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.296][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.297][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:40.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:40.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.302][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:40.303][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:40.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.304][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.306][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:40.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:40.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.310][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:40.311][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:40.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.313][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:40.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:40.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.318][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:40.319][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:40.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.321][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:40.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:40.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.327][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:40.328][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:40.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.330][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.331][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:40.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:40.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.335][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:40.337][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:40.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.338][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.340][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:40.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:40.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:40.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:40.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:40.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:40.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:40.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:40.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:40.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:40.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:40.391][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-11-27 20:40:40.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:40.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:40.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:40.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:40.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:40.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:40.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:40.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:40.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:40.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:40.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:40.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:40.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:40.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:40.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:40.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:40.414][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-11-27 20:40:40.416][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:40.417][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-11-27 20:40:40.418][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:40.420][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:40.421][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:40.422][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:40.423][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:40.424][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:40.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:40.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:40.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:40.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:40.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:40.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:40.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:40.437][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-11-27 20:40:40.440][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:40.441][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:40.443][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-11-27 20:40:40.796][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-11-27 20:40:41.143][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:41.147][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-11-27 20:40:41.153][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-11-27 20:40:41.167][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-11-27 20:40:41.169][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:41.170][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:41.172][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:41.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:41.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:41.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:41.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:41.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:41.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:41.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:41.185][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.186][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.188][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.194][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:41.195][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:41.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.197][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.198][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:41.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:41.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.203][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:41.204][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:41.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.205][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.207][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:41.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:41.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.211][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:41.212][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:41.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.214][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:41.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:41.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.220][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:41.221][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:41.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.223][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:41.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:41.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.228][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:41.229][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:41.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.231][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.233][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:41.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:41.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.237][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:41.238][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:41.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.240][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.241][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:41.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:41.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.245][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:41.246][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:41.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.248][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:41.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:41.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.254][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:41.255][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:41.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.257][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:41.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:41.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.263][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:41.269][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:41.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.272][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.273][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:41.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:41.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.277][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:41.278][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:41.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.280][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.281][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:41.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:41.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:41.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:41.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:41.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:41.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:41.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:41.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:41.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:41.326][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-11-27 20:40:41.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:41.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:41.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:41.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:41.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:41.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:41.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:41.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:41.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:41.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:41.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:41.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:41.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:41.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:41.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:41.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:41.350][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-11-27 20:40:41.351][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:41.353][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-11-27 20:40:41.354][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:41.355][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:41.356][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:41.357][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:41.358][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:41.359][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:41.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:41.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:41.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:41.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:41.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:41.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:41.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:41.379][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-11-27 20:40:41.382][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:41.383][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:41.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-11-27 20:40:41.726][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-11-27 20:40:42.080][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:42.083][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-11-27 20:40:42.086][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-11-27 20:40:42.089][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-11-27 20:40:42.090][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:42.091][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:42.093][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:42.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:42.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:42.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:42.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:42.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:42.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:42.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:42.106][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.108][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.109][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.115][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:42.116][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:42.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.118][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.119][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:42.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:42.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.123][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:42.124][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:42.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.126][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.127][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:42.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:42.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.131][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:42.133][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:42.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.134][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:42.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:42.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.140][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:42.141][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:42.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.143][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:42.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:42.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.148][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:42.149][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:42.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.151][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.152][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:42.154][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:42.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.155][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.157][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:42.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:42.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.171][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:42.172][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:42.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.174][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:42.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:42.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.180][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:42.181][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:42.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.182][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:42.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:42.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.188][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:42.189][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:42.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.191][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.192][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:42.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:42.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.196][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:42.197][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:42.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.199][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.200][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:42.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:42.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:42.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:42.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:42.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:42.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:42.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:42.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:42.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:42.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:42.245][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-11-27 20:40:42.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:42.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:42.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:42.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:42.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:42.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:42.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:42.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:42.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:42.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:42.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:42.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:42.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:42.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:42.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:42.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:42.275][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-11-27 20:40:42.276][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:42.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-11-27 20:40:42.279][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:42.280][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:42.281][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:42.282][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:42.283][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:42.284][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:42.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:42.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:42.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:42.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:42.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:42.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:42.297][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[2024-11-27 20:40:42.298][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-11-27 20:40:42.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:42.302][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:42.304][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-11-27 20:40:42.655][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-11-27 20:40:42.999][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:43.003][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-11-27 20:40:43.008][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-11-27 20:40:43.013][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-11-27 20:40:43.015][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:43.017][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:43.019][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:43.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:43.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:43.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:43.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:43.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:43.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:43.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:43.042][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.044][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.047][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.055][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:43.056][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:43.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.059][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.060][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:43.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:43.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.065][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:43.067][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:43.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.069][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:43.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:43.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.075][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:43.076][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:43.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.078][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:43.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:43.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.083][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:43.094][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:43.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.097][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:43.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:43.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.102][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:43.103][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:43.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.105][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.107][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:43.108][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:43.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.109][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.111][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:43.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:43.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.115][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:43.116][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:43.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.118][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:43.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:43.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.123][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:43.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:43.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.126][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:43.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:43.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.131][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:43.132][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:43.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.134][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.135][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:43.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:43.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.139][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:43.140][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:43.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.142][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:43.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:43.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:43.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:43.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:43.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:43.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:43.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:43.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:43.192][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-11-27 20:40:43.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:43.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:43.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:43.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:43.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:43.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:43.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:43.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:43.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:43.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:43.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:43.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:43.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:43.215][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-11-27 20:40:43.216][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:43.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-11-27 20:40:43.219][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:43.220][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:43.221][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:43.222][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:43.223][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:43.224][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:43.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:43.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:43.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:43.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:43.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:43.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:43.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:43.237][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-11-27 20:40:43.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:43.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:43.242][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-11-27 20:40:43.585][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-11-27 20:40:43.930][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:43.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-11-27 20:40:43.936][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-11-27 20:40:43.939][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-11-27 20:40:43.940][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:43.941][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:43.942][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:43.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:43.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:43.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:43.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:43.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:43.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:43.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:43.956][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.957][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.959][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:43.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:43.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.964][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:43.966][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:43.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.968][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.970][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:43.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:43.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.984][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:43.986][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:43.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.988][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.989][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:43.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:43.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.993][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:43.994][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:43.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:43.996][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:43.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:43.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:44.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.002][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:44.003][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:44.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.005][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:44.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:44.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.010][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:44.011][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:44.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.013][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.015][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:44.016][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.018][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.019][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:44.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.023][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:44.024][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:44.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.026][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:44.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:44.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.031][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:44.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:44.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.035][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:44.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:44.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.040][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:44.041][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:44.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.043][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.045][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:44.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:44.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.049][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:44.050][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:44.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.052][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.053][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:44.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:44.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:44.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:44.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:44.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:44.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:44.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:44.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:44.104][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-11-27 20:40:44.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:44.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:44.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:44.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:44.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:44.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:44.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:44.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:44.128][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-11-27 20:40:44.129][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:44.131][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-11-27 20:40:44.132][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:44.133][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:44.134][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:44.135][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:44.137][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:44.137][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:44.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:44.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:44.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:44.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:44.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:44.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:44.151][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[2024-11-27 20:40:44.153][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-11-27 20:40:44.156][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:44.157][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:44.158][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-11-27 20:40:44.504][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-11-27 20:40:44.851][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:44.855][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-11-27 20:40:44.862][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-11-27 20:40:44.868][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-11-27 20:40:44.871][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:44.873][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:44.876][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:44.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:44.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:44.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:44.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:44.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:44.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:44.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:44.913][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.914][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.917][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:44.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:44.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.924][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:44.925][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:44.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.927][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.929][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:44.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:44.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.933][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:44.934][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:44.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.936][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.938][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:44.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:44.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.942][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:44.943][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:44.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.945][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:44.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:44.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.950][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:44.951][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:44.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.953][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.954][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:44.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:44.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.958][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:44.959][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:44.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.961][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.962][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:44.963][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.965][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.966][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:44.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:44.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.970][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:44.971][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:44.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.973][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:44.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:44.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.978][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:44.979][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:44.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.981][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.982][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:44.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:44.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.986][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:44.987][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:44.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.989][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.990][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:44.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:44.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.994][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:44.995][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:44.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:44.997][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:44.998][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:44.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:45.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:45.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:45.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:45.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:45.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:45.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:45.052][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-11-27 20:40:45.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:45.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:45.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:45.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:45.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:45.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:45.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:45.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:45.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:45.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:45.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:45.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:45.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:45.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:45.081][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-11-27 20:40:45.082][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:45.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-11-27 20:40:45.086][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:45.087][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:45.088][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:45.089][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:45.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:45.092][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:45.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:45.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:45.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:45.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:45.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:45.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:45.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:45.108][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-11-27 20:40:45.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:45.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:45.114][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-11-27 20:40:45.473][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-11-27 20:40:45.825][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-11-27 20:40:45.831][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-11-27 20:40:45.836][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-11-27 20:40:45.846][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-11-27 20:40:45.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-11-27 20:40:45.859][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:45.863][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:45.866][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:45.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:45.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:45.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:45.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:45.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:45.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:45.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:45.894][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.899][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:45.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:45.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.907][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:45.908][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:45.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.910][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.912][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:45.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.916][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:45.917][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:45.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.919][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:45.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:45.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.924][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:45.925][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:45.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.927][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:45.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:45.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:45.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:45.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.936][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:45.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:45.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.941][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:45.942][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:45.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.944][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.945][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:45.947][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:45.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.948][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.950][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:45.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:45.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.954][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:45.955][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:45.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.957][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:45.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:45.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.962][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:45.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:45.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.975][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:45.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:45.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.981][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:45.982][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:45.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.984][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.985][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:45.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:45.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.989][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:45.990][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:45.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.992][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.993][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:45.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:45.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:45.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:45.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:45.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:46.038][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-11-27 20:40:46.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:46.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:46.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:46.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:46.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:46.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:46.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:46.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:46.062][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-11-27 20:40:46.063][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:46.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-11-27 20:40:46.066][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:46.075][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:46.077][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:46.079][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:46.080][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:46.081][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:46.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:46.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:46.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:46.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:46.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:46.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:46.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:46.094][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-11-27 20:40:46.097][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:46.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:46.100][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-11-27 20:40:46.444][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-11-27 20:40:46.787][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:46.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-11-27 20:40:46.798][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-11-27 20:40:46.803][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-11-27 20:40:46.806][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:46.809][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:46.811][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:46.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:46.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:46.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:46.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:46.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:46.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:46.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:46.838][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.842][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.851][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:46.852][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:46.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.855][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.856][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:46.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:46.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.861][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:46.863][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:46.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.865][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.866][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:46.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:46.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.871][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:46.872][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:46.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.874][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.875][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:46.877][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:46.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.878][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.880][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:46.881][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:46.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.883][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.884][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:46.885][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.887][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.888][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:46.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.903][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:46.904][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:46.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.906][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:46.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:46.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.912][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:46.913][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:46.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.915][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:46.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:46.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.920][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:46.921][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:46.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.923][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.924][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:46.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.929][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:46.930][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:46.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.931][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:46.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:46.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:46.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:46.973][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-11-27 20:40:46.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:46.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:46.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:46.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:46.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:46.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:46.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:46.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:46.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:46.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:46.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:47.003][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-11-27 20:40:47.004][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:47.006][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-11-27 20:40:47.007][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:47.008][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:47.009][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:47.010][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:47.011][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:47.012][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:47.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:47.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:47.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:47.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:47.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:47.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:47.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:47.026][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-11-27 20:40:47.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:47.029][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:47.031][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-11-27 20:40:47.380][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-11-27 20:40:47.729][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:47.731][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-11-27 20:40:47.735][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-11-27 20:40:47.737][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-11-27 20:40:47.738][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:47.740][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:47.741][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:47.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:47.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:47.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:47.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:47.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:47.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:47.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:47.754][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.755][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.757][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.762][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:47.763][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:47.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.765][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.767][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:47.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:47.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.771][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:47.772][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:47.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.774][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:47.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:47.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.779][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:47.780][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:47.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.782][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.783][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:47.785][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:47.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.786][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.788][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:47.789][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:47.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.791][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.792][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:47.793][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:47.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.805][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.806][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:47.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:47.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.811][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:47.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:47.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.814][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:47.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:47.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.819][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:47.820][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:47.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.822][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:47.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:47.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.827][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:47.829][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:47.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.830][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:47.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:47.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.836][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:47.837][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:47.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.838][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:47.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:47.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:47.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:47.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:47.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:47.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:47.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:47.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:47.880][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-11-27 20:40:47.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:47.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:47.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:47.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:47.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:47.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:47.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:47.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:47.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:47.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:47.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:47.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:47.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:47.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:47.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:47.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:47.910][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-11-27 20:40:47.911][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:47.912][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-11-27 20:40:47.914][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:47.915][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:47.916][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:47.917][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:47.918][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:47.919][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:47.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:47.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:47.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:47.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:47.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:47.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:47.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:47.932][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-11-27 20:40:47.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:47.936][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:47.937][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-11-27 20:40:48.295][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-11-27 20:40:48.654][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-11-27 20:40:48.657][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-11-27 20:40:48.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-11-27 20:40:48.666][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-11-27 20:40:48.670][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-11-27 20:40:48.672][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:48.675][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:48.677][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:48.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:48.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:48.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:48.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:48.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:48.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:48.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:48.700][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.702][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.705][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.712][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:48.714][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:48.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.716][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.718][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:48.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:48.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.723][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:48.724][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:48.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.726][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.728][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:48.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:48.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.732][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:48.733][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:48.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.735][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:48.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:48.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.751][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:48.752][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:48.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.754][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:48.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:48.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.760][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:48.761][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:48.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.763][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.764][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:48.765][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:48.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.767][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.768][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:48.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:48.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.772][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:48.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:48.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.775][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:48.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:48.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.780][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:48.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:48.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.783][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:48.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:48.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.789][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:48.790][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:48.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.792][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.793][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:48.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:48.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.797][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:48.798][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:48.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.800][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.801][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:48.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:48.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:48.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:48.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:48.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:48.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:48.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:48.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:48.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:48.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:48.853][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-11-27 20:40:48.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:48.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:48.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:48.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:48.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:48.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:48.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:48.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:48.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:48.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:48.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:48.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:48.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:48.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:48.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:48.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:48.876][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-11-27 20:40:48.877][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:48.878][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-11-27 20:40:48.880][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:48.881][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:48.882][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:48.883][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:48.884][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:48.885][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:48.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:48.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:48.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:48.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:48.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:48.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:48.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:48.898][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-11-27 20:40:48.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:48.902][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:48.904][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-11-27 20:40:49.255][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-11-27 20:40:49.597][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:49.601][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-11-27 20:40:49.606][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-11-27 20:40:49.613][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-11-27 20:40:49.616][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:49.618][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:49.620][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:49.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:49.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:49.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:49.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:49.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:49.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:49.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:49.643][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.645][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.648][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.655][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:49.656][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:49.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.658][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.670][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:49.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:49.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.675][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:49.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:49.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.678][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.679][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:49.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:49.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.683][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:49.684][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:49.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.686][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:49.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:49.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.691][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:49.692][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:49.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.694][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:49.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:49.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.699][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:49.700][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:49.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.702][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.703][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:49.704][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:49.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.706][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.707][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:49.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:49.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.711][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:49.712][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:49.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.714][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:49.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:49.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.719][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:49.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:49.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.722][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:49.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:49.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.727][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:49.728][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:49.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.730][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.731][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:49.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:49.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.735][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:49.736][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:49.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.738][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.739][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:49.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:49.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:49.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:49.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:49.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:49.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:49.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:49.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:49.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:49.786][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-11-27 20:40:49.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:49.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:49.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:49.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:49.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:49.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:49.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:49.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:49.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:49.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:49.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:49.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:49.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:49.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:49.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:49.809][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-11-27 20:40:49.810][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:49.812][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-11-27 20:40:49.813][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:49.814][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:49.815][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:49.816][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:49.817][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:49.818][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:49.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:49.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:49.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:49.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:49.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:49.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:49.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:49.830][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-11-27 20:40:49.833][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:49.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:49.835][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-11-27 20:40:50.196][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-11-27 20:40:50.547][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:50.552][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-11-27 20:40:50.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-11-27 20:40:50.565][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-11-27 20:40:50.568][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:50.571][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:50.573][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:50.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:50.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:50.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:50.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:50.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:50.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:50.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:50.610][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.612][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.615][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.628][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:50.630][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:50.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.633][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.636][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:50.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:50.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.642][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:50.644][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:50.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.646][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:50.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:50.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.653][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:50.654][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:50.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.657][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:50.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:50.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.663][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:50.664][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:50.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.666][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:50.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:50.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.672][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:50.673][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:50.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.676][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.677][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:50.679][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:50.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.681][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.682][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:50.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:50.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:50.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:50.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.690][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:50.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:50.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.696][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:50.697][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:50.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.699][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:50.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.705][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:50.706][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:50.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.708][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.710][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:50.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:50.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.714][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:50.715][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:50.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.717][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.719][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:50.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:50.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:50.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:50.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:50.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:50.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:50.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:50.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:50.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:50.783][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-11-27 20:40:50.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:50.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:50.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:50.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:50.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:50.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:50.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:50.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:50.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:50.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:50.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:50.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:50.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:50.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:50.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:50.804][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[2024-11-27 20:40:50.805][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-11-27 20:40:50.806][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:50.808][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-11-27 20:40:50.809][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:50.810][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:50.811][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:50.812][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:50.813][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:50.814][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:50.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:50.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:50.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:50.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:50.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:50.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:50.826][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[2024-11-27 20:40:50.827][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-11-27 20:40:50.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:50.835][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:50.836][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-11-27 20:40:51.188][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-11-27 20:40:51.538][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:51.543][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-11-27 20:40:51.550][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-11-27 20:40:51.556][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-11-27 20:40:51.559][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:51.561][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:51.564][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:51.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:51.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:51.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:51.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:51.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:51.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:51.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:51.587][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.589][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.592][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.601][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:51.602][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:51.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.605][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.607][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:51.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:51.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.614][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:51.615][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:51.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.618][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.620][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:51.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:51.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.624][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:51.625][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:51.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.627][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.628][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:51.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:51.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.632][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:51.633][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:51.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.635][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:51.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:51.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.641][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:51.642][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:51.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.644][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.645][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:51.646][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:51.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.648][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.649][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:51.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:51.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.653][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:51.654][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:51.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.656][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:51.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:51.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.662][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:51.673][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:51.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.676][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:51.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:51.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.681][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:51.682][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:51.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.684][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.686][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:51.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:51.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.690][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:51.691][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:51.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.693][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.694][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:51.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:51.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:51.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:51.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:51.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:51.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:51.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:51.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:51.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:51.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:51.739][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-11-27 20:40:51.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:51.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:51.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:51.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:51.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:51.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:51.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:51.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:51.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:51.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:51.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:51.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:51.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:51.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:51.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:51.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:51.763][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-11-27 20:40:51.764][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:51.766][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-11-27 20:40:51.773][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:51.774][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:51.775][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:51.777][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:51.778][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:51.779][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:51.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:51.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:51.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:51.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:51.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:51.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:51.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:51.792][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-11-27 20:40:51.795][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:51.796][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:51.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-11-27 20:40:52.165][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-11-27 20:40:52.511][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:52.514][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-11-27 20:40:52.517][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-11-27 20:40:52.519][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-11-27 20:40:52.521][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:52.522][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:52.523][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:52.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:52.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:52.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:52.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:52.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:52.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:52.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:52.537][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.538][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.540][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.545][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:52.546][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:52.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.548][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.549][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:52.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:52.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.554][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:52.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:52.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.557][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:52.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:52.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.562][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:52.563][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:52.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.565][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:52.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:52.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.570][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:52.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:52.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.573][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:52.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:52.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.589][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:52.590][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:52.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.593][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.594][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:52.595][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:52.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.597][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.598][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:52.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:52.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.602][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:52.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:52.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.605][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:52.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:52.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.611][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:52.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:52.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.614][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:52.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:52.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.619][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:52.620][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:52.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.622][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.623][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:52.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:52.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.627][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:52.628][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:52.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.630][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.632][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:52.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:52.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:52.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:52.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:52.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:52.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:52.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:52.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:52.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:52.680][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-11-27 20:40:52.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:52.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:52.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:52.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:52.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:52.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:52.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:52.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:52.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:52.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:52.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:52.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:52.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:52.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:52.727][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-11-27 20:40:52.729][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:52.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-11-27 20:40:52.733][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:52.735][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:52.737][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:52.738][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:52.739][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:52.740][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:52.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:52.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:52.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:52.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:52.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:52.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:52.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:52.755][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-11-27 20:40:52.758][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:52.758][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:52.760][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-11-27 20:40:53.105][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-11-27 20:40:53.452][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:53.456][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-11-27 20:40:53.464][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-11-27 20:40:53.470][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-11-27 20:40:53.473][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:53.476][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:53.479][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:53.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:53.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:53.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:53.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:53.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:53.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:53.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:53.505][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.507][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.510][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.517][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:53.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:53.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.521][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.523][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:53.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:53.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.528][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:53.529][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:53.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.541][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:53.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:53.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.547][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:53.548][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:53.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.550][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:53.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:53.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.555][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:53.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:53.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.558][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:53.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:53.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.563][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:53.564][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:53.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.565][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.567][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:53.568][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:53.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.569][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.570][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:53.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:53.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.574][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:53.575][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:53.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.577][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:53.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:53.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.582][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:53.583][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:53.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.585][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:53.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:53.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.590][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:53.591][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:53.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.593][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:53.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:53.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.598][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:53.599][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:53.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.600][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:53.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:53.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:53.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:53.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:53.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:53.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:53.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:53.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:53.648][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-11-27 20:40:53.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:53.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:53.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:53.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:53.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:53.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:53.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:53.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:53.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:53.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:53.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:53.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:53.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:53.669][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[2024-11-27 20:40:53.671][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-11-27 20:40:53.671][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:53.673][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-11-27 20:40:53.674][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:53.675][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:53.676][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:53.677][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:53.678][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:53.679][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:53.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:53.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:53.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:53.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:53.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:53.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:53.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:53.691][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-11-27 20:40:53.694][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:53.695][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:53.696][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-11-27 20:40:54.038][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-11-27 20:40:54.392][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:54.397][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-11-27 20:40:54.403][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-11-27 20:40:54.407][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-11-27 20:40:54.410][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:54.413][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:54.415][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:54.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:54.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:54.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:54.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:54.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:54.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:54.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:54.448][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.451][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.457][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:54.459][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:54.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.461][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.462][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:54.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:54.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.466][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:54.467][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:54.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.469][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:54.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:54.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.474][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:54.475][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:54.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.477][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:54.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:54.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.482][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:54.483][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:54.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.485][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:54.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:54.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.490][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:54.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:54.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.493][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.494][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:54.495][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:54.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.497][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.498][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:54.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:54.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.502][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:54.503][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:54.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.505][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:54.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:54.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.510][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:54.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:54.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:54.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:54.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.517][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:54.518][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:54.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.521][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:54.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:54.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.525][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:54.526][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:54.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.528][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.529][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:54.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:54.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:54.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:54.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:54.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:54.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:54.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:54.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:54.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:54.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:54.740][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-11-27 20:40:54.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:54.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:54.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:54.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:54.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:54.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:54.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:54.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:54.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:54.767][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:54.770][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:54.771][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:54.773][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:40:55.348][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:40:55.867][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:55.869][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-27 20:40:55.872][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-11-27 20:40:55.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:55.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:55.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:55.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:55.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:55.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:55.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:55.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:55.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:55.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:55.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:55.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:55.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:55.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:55.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:55.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:55.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:55.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:55.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:55.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:55.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:55.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:55.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:55.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:55.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:55.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:55.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:55.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:55.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:55.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:55.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:55.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:55.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:55.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:55.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:55.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:55.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:55.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:56.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:56.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:56.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:56.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:56.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:56.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:56.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:56.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:56.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:56.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:56.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:56.404][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:56.407][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:56.408][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:56.410][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:40:56.753][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:40:57.104][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:57.107][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-11-27 20:40:57.111][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-11-27 20:40:57.115][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:57.118][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:57.119][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:57.121][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:40:57.481][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:40:57.826][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:57.831][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-11-27 20:40:57.840][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-11-27 20:40:57.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:57.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:57.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:57.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:57.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:57.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:57.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:57.869][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-11-27 20:40:57.871][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:57.874][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-11-27 20:40:57.877][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:57.879][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:57.880][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:57.882][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:57.884][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:57.885][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:57.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:57.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:57.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:57.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:57.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:57.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:57.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:57.903][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-11-27 20:40:57.906][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:57.908][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:57.909][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-11-27 20:40:58.257][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-11-27 20:40:58.609][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:58.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-11-27 20:40:58.622][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-11-27 20:40:58.629][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-11-27 20:40:58.632][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:58.635][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:58.638][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:58.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:58.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:58.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:58.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:58.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:58.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:58.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:58.681][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.683][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.685][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.691][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:58.692][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:58.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.694][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.696][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:58.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:58.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.700][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:58.701][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:58.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.703][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:58.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:58.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.708][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:58.709][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:58.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.710][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:58.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:58.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.715][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:58.716][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:58.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.718][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:58.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:58.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.723][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:58.724][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:58.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.726][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.727][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:58.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:58.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.731][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:58.732][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:58.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.733][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.734][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:58.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:58.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.738][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.739][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.741][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.746][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:58.747][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:58.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.748][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:58.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:58.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.753][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:58.754][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:58.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.756][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.757][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:58.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:58.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.761][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:58.762][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:58.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.764][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.765][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:58.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:58.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:58.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:58.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:58.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:58.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:58.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:58.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:58.807][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-11-27 20:40:58.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:58.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:58.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:58.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:58.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:58.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:58.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:58.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:58.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:58.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:58.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:58.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:58.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:58.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:58.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:58.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:58.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:58.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:58.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:58.851][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-11-27 20:40:58.852][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:40:58.853][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-11-27 20:40:58.855][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:40:58.856][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:40:58.857][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:40:58.858][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:40:58.859][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:40:58.859][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:40:58.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:58.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:58.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:58.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:58.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:58.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:58.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:40:58.872][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-11-27 20:40:58.875][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:40:58.876][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:40:58.877][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-11-27 20:40:59.223][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-11-27 20:40:59.572][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:40:59.577][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-11-27 20:40:59.584][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-11-27 20:40:59.590][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-11-27 20:40:59.593][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:40:59.595][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:40:59.598][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:40:59.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.619][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.TRACE[2024-11-27 20:40:59.623][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.624][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.627][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.635][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:59.636][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:59.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.639][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.640][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:40:59.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:40:59.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.645][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:59.646][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:59.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.648][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:40:59.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:40:59.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.654][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:59.655][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:59.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.657][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:40:59.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:40:59.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.662][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:59.663][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:59.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.665][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:40:59.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:40:59.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.670][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:59.671][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:40:59.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.673][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.674][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:59.675][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:59.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.677][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.678][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:40:59.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:40:59.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.682][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.683][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.685][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.690][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:59.691][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:59.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.692][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:40:59.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:40:59.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.698][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:59.699][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:59.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.700][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.701][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:40:59.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:40:59.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.705][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:59.706][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:59.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.708][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.709][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:40:59.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:40:59.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:59.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:59.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:59.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:59.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:40:59.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:40:59.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:40:59.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:40:59.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.759][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-11-27 20:40:59.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.786][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:40:59.789][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:40:59.790][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:40:59.792][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:40:59.793][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:40:59.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:40:59.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:40:59.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:40:59.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:40:59.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:40:59.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:40:59.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:40:59.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:40:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:40:59.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:40:59.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:40:59.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.269][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:00.272][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:00.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:41:00.275][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:00.276][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:41:00.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:00.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:00.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.824][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-27 20:41:00.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-27 20:41:00.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:41:00.835][biodb::testThat]
biodb.INFO [2024-11-27 20:41:00.836][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-11-27 20:41:00.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:00.838][biodb::testThat]
biodb.TRACE[2024-11-27 20:41:00.841][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-27 20:41:00.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-27 20:41:00.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:00.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:00.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:00.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:00.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:00.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:00.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:00.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:00.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:00.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:00.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:00.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:00.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:00.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:00.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:00.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:00.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:00.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:00.881][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:00.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:00.885][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:00.887][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:01.241][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:01.585][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:01.587][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-11-27 20:41:01.591][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-11-27 20:41:01.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:01.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:01.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:01.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:01.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:01.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:01.602][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.TRACE[2024-11-27 20:41:01.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:01.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:01.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:01.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:01.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:01.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:01.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:01.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:01.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:01.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:01.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:01.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:01.616][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:01.619][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:01.620][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:01.622][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:01.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:02.311][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:02.314][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-11-27 20:41:02.320][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-11-27 20:41:02.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:02.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:02.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:02.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:02.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:02.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:02.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:02.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:02.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:02.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:02.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:02.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:02.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:02.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:02.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:02.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:02.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:02.386][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:41:02.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:02.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:02.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:02.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:02.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:02.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:02.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:02.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.405][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.405][private$selectFields]
biodb.TRACE[2024-11-27 20:41:02.406][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:02.407][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:02.408][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.412][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.413][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.414][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.415][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.417][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.421][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.422][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:02.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.443][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-27 20:41:02.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:02.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:02.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:02.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:02.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:02.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:02.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:02.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.462][private$selectFields]
biodb.TRACE[2024-11-27 20:41:02.463][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:02.463][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:02.464][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.465][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.466][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.468][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.469][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.470][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.472][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.474][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.475][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.477][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.478][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:02.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.491][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:41:02.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:02.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:02.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:02.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:02.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:02.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:02.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:02.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.509][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.509][private$selectFields]
biodb.TRACE[2024-11-27 20:41:02.510][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:02.511][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:02.512][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.516][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.517][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.518][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.519][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.520][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.521][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:02.522][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.523][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.525][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.526][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:02.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:02.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.538][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-27 20:41:02.539][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:41:02.540][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:41:02.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:02.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:02.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:02.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:02.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:02.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:02.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:02.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:02.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:02.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:02.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:02.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:02.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:02.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:02.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:02.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:02.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:02.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:02.635][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:02.638][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:02.639][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:02.641][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:02.989][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:03.335][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:03.337][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-11-27 20:41:03.341][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-11-27 20:41:03.347][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:03.354][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:03.356][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:03.360][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:03.722][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:04.083][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:04.089][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-11-27 20:41:04.099][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-11-27 20:41:04.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.235][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:41:04.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.283][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.284][private$selectFields]
biodb.TRACE[2024-11-27 20:41:04.285][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:04.286][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:04.287][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.289][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.290][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.292][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.293][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.294][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.296][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.297][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.298][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.299][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.303][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.304][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:04.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.318][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-27 20:41:04.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.378][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.380][private$selectFields]
biodb.TRACE[2024-11-27 20:41:04.381][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:04.382][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:04.383][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.384][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.385][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.387][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.391][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.392][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.403][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.404][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.405][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.407][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.408][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:04.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.441][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:41:04.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.462][private$selectFields]
biodb.TRACE[2024-11-27 20:41:04.463][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:04.464][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:04.465][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.466][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.467][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.468][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.469][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.472][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.474][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.475][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.476][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.478][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.479][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:04.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.493][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-27 20:41:04.493][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:41:04.494][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:41:04.502][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-27 20:41:04.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-27 20:41:04.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:41:04.509][biodb::testThat]
biodb.INFO [2024-11-27 20:41:04.509][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-11-27 20:41:04.510][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:04.511][biodb::testThat]
biodb.TRACE[2024-11-27 20:41:04.514][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-27 20:41:04.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-27 20:41:04.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:04.545][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:04.548][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:04.550][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-27 20:41:04.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:04.552][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-27 20:41:04.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.575][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:04.578][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:04.579][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-27 20:41:04.581][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:04.582][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-27 20:41:04.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:04.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.625][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:41:04.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.645][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.646][private$selectFields]
biodb.TRACE[2024-11-27 20:41:04.647][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:04.648][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:04.649][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.651][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.652][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.653][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.654][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.656][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.657][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.658][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.659][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.660][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.662][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.663][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:04.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.675][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-27 20:41:04.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.684][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[2024-11-27 20:41:04.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.693][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.694][private$selectFields]
biodb.TRACE[2024-11-27 20:41:04.695][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:04.696][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:04.697][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.697][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.698][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.700][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.701][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.702][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.704][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.705][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.706][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.707][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.708][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.709][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.710][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:04.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.723][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:41:04.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.741][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.741][private$selectFields]
biodb.TRACE[2024-11-27 20:41:04.742][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:04.743][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:04.744][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.745][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.746][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.748][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.749][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.750][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.751][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.753][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.754][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.755][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.757][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.758][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:04.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.775][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-27 20:41:04.776][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:41:04.777][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:41:04.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:04.811][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:04.814][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:04.815][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-27 20:41:04.816][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:04.817][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-27 20:41:04.820][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:04.823][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:04.824][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-27 20:41:04.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:04.826][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-27 20:41:04.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:04.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:04.889][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:41:04.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.907][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.908][private$selectFields]
biodb.TRACE[2024-11-27 20:41:04.909][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:04.910][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:04.911][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.912][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.914][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.915][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.916][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.918][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.919][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.920][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.921][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.922][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.923][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.924][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:04.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.936][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-27 20:41:04.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.954][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.955][private$selectFields]
biodb.TRACE[2024-11-27 20:41:04.956][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:04.957][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:04.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.960][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.961][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.962][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.963][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.965][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.966][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.967][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:04.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.971][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.971][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:04.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.984][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:41:04.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:04.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:04.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:04.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:04.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:04.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:04.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:04.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:04.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:04.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:04.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.002][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.002][private$selectFields]
biodb.TRACE[2024-11-27 20:41:05.003][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:05.004][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:05.005][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.006][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.007][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.009][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.010][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.011][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.012][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.014][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.016][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.018][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.019][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:05.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.031][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-27 20:41:05.032][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:41:05.033][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:41:05.041][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-27 20:41:05.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-27 20:41:05.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:41:05.047][biodb::testThat]
biodb.INFO [2024-11-27 20:41:05.048][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-11-27 20:41:05.049][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:05.050][biodb::testThat]
biodb.TRACE[2024-11-27 20:41:05.052][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-27 20:41:05.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-27 20:41:05.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:05.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:05.085][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:05.088][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:05.089][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-27 20:41:05.090][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:05.092][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-27 20:41:05.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:05.119][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:05.122][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:05.123][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-27 20:41:05.124][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:05.125][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-27 20:41:05.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:05.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:05.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:05.168][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:41:05.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.186][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.187][private$selectFields]
biodb.TRACE[2024-11-27 20:41:05.188][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:05.189][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:05.190][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.190][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.191][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.193][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.194][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.195][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.197][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.198][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.199][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.200][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.201][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.202][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.203][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:05.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.215][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-27 20:41:05.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.242][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.243][private$selectFields]
biodb.TRACE[2024-11-27 20:41:05.244][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:05.245][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:05.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.247][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.250][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.254][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.255][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.256][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.257][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.259][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.261][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.262][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:05.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.276][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:41:05.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.298][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.299][private$selectFields]
biodb.TRACE[2024-11-27 20:41:05.300][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:05.301][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:05.301][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.303][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.304][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.306][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.307][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.308][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.310][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.311][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.312][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.314][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.316][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.317][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:05.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.330][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-27 20:41:05.331][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:41:05.332][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:41:05.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:05.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:05.385][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:05.388][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:05.390][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-27 20:41:05.391][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:05.392][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-27 20:41:05.396][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:05.399][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:05.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-27 20:41:05.401][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:05.403][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-27 20:41:05.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:05.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:05.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:05.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:05.485][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:41:05.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.504][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.505][private$selectFields]
biodb.TRACE[2024-11-27 20:41:05.506][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:05.507][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:05.508][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.509][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.510][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.516][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.517][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.518][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.519][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.522][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.523][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:05.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.536][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-27 20:41:05.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.555][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.556][private$selectFields]
biodb.TRACE[2024-11-27 20:41:05.557][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:05.558][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:05.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.560][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.561][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.562][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.563][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.564][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.566][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.567][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.568][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.569][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.572][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.573][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:05.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.587][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:41:05.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:05.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.607][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.607][private$selectFields]
biodb.TRACE[2024-11-27 20:41:05.608][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:41:05.609][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:41:05.610][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.611][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.614][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.615][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.617][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.618][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.619][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:41:05.620][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.621][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.623][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.624][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:41:05.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:05.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:05.636][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-27 20:41:05.637][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:41:05.638][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:41:05.654][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-27 20:41:05.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-27 20:41:05.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:05.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:41:05.660][biodb::testThat]
biodb.INFO [2024-11-27 20:41:05.661][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-11-27 20:41:05.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:05.663][biodb::testThat]
biodb.DEBUG[2024-11-27 20:41:05.664][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-11-27 20:41:05.665][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:41:05.667][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-11-27 20:41:05.668][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:41:05.669][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:41:05.670][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:41:05.671][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:41:05.672][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:41:05.673][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:41:05.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:05.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:05.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:05.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:05.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:05.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:05.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:05.684][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-11-27 20:41:05.687][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:05.688][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:05.689][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-11-27 20:41:06.038][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-11-27 20:41:06.382][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:06.386][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-11-27 20:41:06.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-11-27 20:41:06.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-11-27 20:41:06.401][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:41:06.404][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:41:06.406][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:41:06.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:06.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:06.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:06.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:06.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:06.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:06.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:06.432][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.433][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.436][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.444][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:41:06.446][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:41:06.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.448][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.450][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:41:06.451][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:41:06.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.454][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.455][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:41:06.457][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:41:06.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.459][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.460][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:41:06.461][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:41:06.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.463][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.465][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:06.466][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:06.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.468][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.469][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:41:06.470][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:06.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.472][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.473][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:06.474][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:06.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.476][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.477][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:06.478][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:06.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.480][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.482][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:41:06.483][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:41:06.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.484][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.486][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:41:06.487][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:41:06.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.488][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:06.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:06.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:06.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:06.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:06.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:06.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:06.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:06.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:06.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:06.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:06.529][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-11-27 20:41:06.530][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-11-27 20:41:06.538][biodb::testThat]
biodb.INFO [2024-11-27 20:41:06.539][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-11-27 20:41:06.540][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:06.550][biodb::testThat]
biodb.DEBUG[2024-11-27 20:41:06.559][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-11-27 20:41:06.561][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-11-27 20:41:06.562][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-11-27 20:41:06.563][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-11-27 20:41:06.564][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-11-27 20:41:06.566][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:41:06.567][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:41:06.568][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:41:06.569][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:41:06.569][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:41:06.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:06.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:06.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:06.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:06.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:06.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:06.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:06.583][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-11-27 20:41:06.586][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:06.587][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:06.589][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-11-27 20:41:06.930][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-11-27 20:41:07.279][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:07.283][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-11-27 20:41:07.290][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-11-27 20:41:07.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:07.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:07.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:07.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:07.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:07.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:07.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:07.315][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-11-27 20:41:07.320][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:07.322][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:07.325][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-11-27 20:41:07.669][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-11-27 20:41:08.018][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:08.023][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-11-27 20:41:08.030][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-11-27 20:41:08.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:08.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:08.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:08.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:08.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:08.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:08.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:08.057][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-11-27 20:41:08.063][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:08.064][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:08.067][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-11-27 20:41:08.419][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-11-27 20:41:08.777][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:08.789][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-11-27 20:41:08.804][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-11-27 20:41:08.813][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-11-27 20:41:08.819][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:41:08.823][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-11-27 20:41:08.826][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-11-27 20:41:08.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:08.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:08.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:08.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:08.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:08.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:08.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:08.864][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:08.866][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:08.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.868][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:08.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:08.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.876][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:41:08.877][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:41:08.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.880][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.882][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:41:08.883][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:41:08.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.886][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:41:08.889][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:41:08.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.891][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.893][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:41:08.894][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:41:08.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.897][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.898][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:08.900][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:08.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.902][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.904][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:41:08.905][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:08.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.908][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.909][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:08.911][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:08.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.913][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.915][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:08.916][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:08.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.919][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.920][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:41:08.922][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:41:08.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.924][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.925][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:41:08.927][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:41:08.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.929][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:08.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:08.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:08.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:08.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:08.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:08.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:08.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:08.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:08.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:08.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:08.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:08.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:08.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:08.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:08.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:08.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:08.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:08.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:08.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:08.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:08.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:08.984][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:08.985][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:08.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.987][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:08.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:08.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.994][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:41:08.995][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:41:08.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:08.998][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:08.999][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:41:09.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:41:09.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.005][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:41:09.006][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:41:09.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.009][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.010][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:41:09.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:41:09.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.015][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:41:09.017][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:41:09.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.019][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.021][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:41:09.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:41:09.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.026][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:41:09.027][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:41:09.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.030][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:41:09.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:41:09.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.037][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:09.038][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:09.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.040][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.042][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:09.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:09.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.047][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:41:09.048][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:09.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.051][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.052][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:41:09.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:09.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.057][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:09.059][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:09.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.061][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:09.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:09.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.068][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:09.069][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:09.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.072][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:09.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:09.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.078][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:41:09.080][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:41:09.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.082][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.083][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:41:09.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:41:09.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.089][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:41:09.090][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:41:09.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.092][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.094][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:41:09.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:41:09.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:09.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:09.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:09.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:09.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:09.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:09.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:09.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:09.148][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.150][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.152][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.159][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:41:09.160][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:41:09.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.162][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.164][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:41:09.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:41:09.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.214][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:41:09.215][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:41:09.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.217][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.219][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:41:09.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:41:09.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.224][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:41:09.225][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:41:09.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.228][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:41:09.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:41:09.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.235][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:41:09.236][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:41:09.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.238][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:41:09.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:41:09.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.245][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:09.246][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:09.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.249][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.250][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:09.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:09.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.255][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:41:09.257][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:09.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.259][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.260][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:41:09.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:09.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.266][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:09.267][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:09.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.270][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:09.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:09.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.276][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:09.277][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:09.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.280][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:09.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:09.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.287][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:41:09.288][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:41:09.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.291][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.292][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:41:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:41:09.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.297][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:41:09.298][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:41:09.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.301][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.302][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:41:09.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:41:09.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:09.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:09.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:09.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:09.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:09.371][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-11-27 20:41:09.372][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-11-27 20:41:09.373][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-11-27 20:41:09.385][biodb::testThat]
biodb.INFO [2024-11-27 20:41:09.386][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-11-27 20:41:09.387][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:09.388][biodb::testThat]
biodb.INFO [2024-11-27 20:41:09.410][biodb::testThat]
biodb.INFO [2024-11-27 20:41:09.411][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-11-27 20:41:09.412][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:09.413][biodb::testThat]
biodb.INFO [2024-11-27 20:41:09.420][biodb::testThat]
biodb.INFO [2024-11-27 20:41:09.421][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-11-27 20:41:09.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:09.423][biodb::testThat]
biodb.DEBUG[2024-11-27 20:41:09.425][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:09.428][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:09.429][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:09.431][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:09.864][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:10.394][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:10.399][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-11-27 20:41:10.408][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-11-27 20:41:10.430][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:10.432][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:10.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:10.436][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:10.437][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:10.439][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:10.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:10.442][ef$get] fields variable is a list.
biodb.INFO [2024-11-27 20:41:10.445][biodb::testThat]
biodb.INFO [2024-11-27 20:41:10.446][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-11-27 20:41:10.447][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:10.449][biodb::testThat]
biodb.ERROR[2024-11-27 20:41:10.465][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-11-27 20:41:10.482][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-11-27 20:41:10.495][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-27 20:41:10.496][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-27 20:41:10.497][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-27 20:41:10.498][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-27 20:41:10.499][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:10.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:10.500][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.502][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:41:10.512][biodb::testContext]
biodb.INFO [2024-11-27 20:41:10.513][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:41:10.514][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-11-27 20:41:10.515][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:41:10.516][biodb::testContext]
biodb.INFO [2024-11-27 20:41:10.518][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:41:10.520][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-27 20:41:10.524][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:10.524][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-27 20:41:10.526][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-27 20:41:10.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.529][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-27 20:41:10.530][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-27 20:41:10.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.534][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-27 20:41:10.534][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-27 20:41:10.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.538][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-27 20:41:10.539][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-27 20:41:10.540][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-27 20:41:10.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.543][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-27 20:41:10.544][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-27 20:41:10.545][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-27 20:41:10.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.549][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-27 20:41:10.550][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-27 20:41:10.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.553][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-27 20:41:10.554][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-27 20:41:10.555][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-27 20:41:10.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.559][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-27 20:41:10.560][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-27 20:41:10.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.571][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.DEBUG[2024-11-27 20:41:10.572][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-27 20:41:10.573][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-27 20:41:10.574][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-27 20:41:10.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.577][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:41:10.578][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-27 20:41:10.579][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-27 20:41:10.580][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-27 20:41:10.581][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-27 20:41:10.582][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-27 20:41:10.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.585][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-27 20:41:10.586][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-27 20:41:10.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.589][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-27 20:41:10.590][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-27 20:41:10.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.594][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-27 20:41:10.594][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-27 20:41:10.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.598][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-27 20:41:10.599][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-27 20:41:10.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.602][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-27 20:41:10.603][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-27 20:41:10.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.606][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:41:10.607][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-27 20:41:10.611][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-27 20:41:10.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.614][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-27 20:41:10.615][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-27 20:41:10.616][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-27 20:41:10.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.620][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-27 20:41:10.622][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.637][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-27 20:41:10.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:10.640][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.641][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.641][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.642][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.643][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:41:10.644][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:10.645][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.646][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-27 20:41:10.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:10.648][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.649][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.650][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:10.650][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:10.650][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:10.650][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:41:10.650][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:41:10.651][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:10.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:10.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:10.653][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:10.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:10.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:10.656][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.657][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.658][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:10.658][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:10.659][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.660][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.661][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-27 20:41:10.663][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.664][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:41:10.665][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:10.667][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.669][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.671][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:41:10.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:10.672][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.673][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-27 20:41:10.674][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:10.675][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.676][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.677][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:10.677][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:10.677][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:10.677][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:41:10.677][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:41:10.678][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:10.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:10.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:10.681][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:10.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:10.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:10.683][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.684][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.685][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:10.686][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:10.687][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.688][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.689][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-27 20:41:10.690][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.691][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-27 20:41:10.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:10.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.696][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.697][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.698][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:41:10.699][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:10.700][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.701][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-27 20:41:10.702][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:10.703][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.703][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.704][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.705][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:10.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:10.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:10.708][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:10.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:10.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:10.711][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.711][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.712][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:10.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:10.714][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.715][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.716][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-27 20:41:10.718][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.719][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:41:10.720][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.721][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:10.721][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.722][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.723][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.724][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.725][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:41:10.726][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:10.727][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.728][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-27 20:41:10.729][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:10.730][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.731][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:10.732][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.733][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:10.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:10.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:10.735][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:10.736][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:10.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:10.738][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:10.739][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.740][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:10.741][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:10.741][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:10.742][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:10.744][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:10.744][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.815][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[2024-11-27 20:41:10.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.820][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[2024-11-27 20:41:10.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.830][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-27 20:41:10.832][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-27 20:41:10.834][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-27 20:41:10.835][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-27 20:41:10.837][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:41:10.838][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-27 20:41:10.839][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-27 20:41:10.841][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-27 20:41:10.842][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-27 20:41:10.844][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-27 20:41:10.845][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:41:10.847][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-27 20:41:10.848][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-27 20:41:10.850][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-27 20:41:10.851][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-27 20:41:10.852][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-27 20:41:10.854][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-27 20:41:10.855][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-27 20:41:10.857][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:41:10.858][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-27 20:41:10.860][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-27 20:41:10.861][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-27 20:41:10.863][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-27 20:41:10.864][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-27 20:41:10.865][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-27 20:41:10.867][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-27 20:41:10.868][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-27 20:41:10.870][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-27 20:41:10.871][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-27 20:41:10.873][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-27 20:41:10.874][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-27 20:41:10.875][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-27 20:41:10.877][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-27 20:41:10.878][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-27 20:41:10.880][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-27 20:41:10.881][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-27 20:41:10.882][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-27 20:41:10.884][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-27 20:41:10.885][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-27 20:41:10.887][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-27 20:41:10.888][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-27 20:41:10.890][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-27 20:41:10.891][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-27 20:41:10.892][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-27 20:41:10.894][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-27 20:41:10.895][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-27 20:41:10.897][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-27 20:41:10.898][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-27 20:41:10.900][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-27 20:41:10.901][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-27 20:41:10.921][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-27 20:41:10.923][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-27 20:41:10.924][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-27 20:41:10.925][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-27 20:41:10.927][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-27 20:41:10.928][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-27 20:41:10.930][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-27 20:41:10.931][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-27 20:41:10.932][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-27 20:41:10.934][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-27 20:41:10.935][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-27 20:41:10.937][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-27 20:41:10.938][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-27 20:41:10.939][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-27 20:41:10.941][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-27 20:41:10.942][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-27 20:41:10.943][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:41:10.945][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:41:10.946][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-27 20:41:10.948][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-27 20:41:10.949][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-27 20:41:10.950][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-27 20:41:10.952][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-27 20:41:10.953][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-27 20:41:10.954][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-27 20:41:10.956][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-27 20:41:10.957][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-27 20:41:10.959][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-27 20:41:10.960][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-27 20:41:10.961][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-27 20:41:10.963][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-27 20:41:10.965][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-27 20:41:10.966][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-27 20:41:10.969][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-27 20:41:10.971][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:41:10.972][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:10.973][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.975][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:10.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:10.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:10.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:10.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:10.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:10.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:10.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:10.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:10.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:10.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:10.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.042][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[2024-11-27 20:41:11.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.067][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[2024-11-27 20:41:11.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:11.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.086][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[2024-11-27 20:41:11.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:11.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:11.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:11.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:11.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:11.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:11.093][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[2024-11-27 20:41:11.094][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-27 20:41:11.096][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-27 20:41:11.098][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:11.099][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-27 20:41:11.100][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:11.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:11.102][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:11.103][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:11.104][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:11.105][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-27 20:41:11.106][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-27 20:41:11.107][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:11.108][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:11.109][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-27 20:41:11.110][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-27 20:41:11.111][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-27 20:41:11.113][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:11.114][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:11.114][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:11.114][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:11.115][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-27 20:41:11.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:11.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:11.117][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:11.118][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:11.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:11.120][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:11.121][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:41:11.121][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-27 20:41:11.122][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:11.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:11.124][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:11.125][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-27 20:41:11.125][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-27 20:41:11.127][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:41:11.128][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:41:11.130][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-27 20:41:11.131][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:41:11.133][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:41:11.134][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:41:11.138][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-27 20:41:11.139][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-27 20:41:11.140][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-27 20:41:11.142][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-27 20:41:11.143][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:41:11.144][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:41:11.145][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-27 20:41:11.146][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-27 20:41:11.148][biodb::testThat]
biodb.INFO [2024-11-27 20:41:11.149][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-11-27 20:41:11.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:11.151][biodb::testThat]
biodb.DEBUG[2024-11-27 20:41:11.155][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-27 20:41:11.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:11.159][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:11.160][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-11-27 20:41:11.489][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-11-27 20:41:11.903][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:11.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-11-27 20:41:11.909][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-11-27 20:41:11.912][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:11.915][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:11.916][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:11.918][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:12.264][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:12.608][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:12.610][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-11-27 20:41:12.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-11-27 20:41:12.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:12.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:12.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:12.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:12.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:12.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:12.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:12.626][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:12.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:12.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:12.631][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:12.974][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:13.316][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:13.318][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-11-27 20:41:13.322][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-11-27 20:41:13.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:13.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:13.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:13.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:13.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:13.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:13.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:13.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:13.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:13.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:13.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:13.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:13.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:13.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:13.362][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:13.365][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:13.367][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-27 20:41:13.368][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:13.369][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-27 20:41:13.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:13.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:13.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:13.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:13.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:13.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:13.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:13.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:13.398][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:13.399][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-27 20:41:13.400][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:13.401][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-27 20:41:13.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:13.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:13.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:13.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:13.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:13.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:13.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:13.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:13.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:13.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:13.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:13.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:13.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:13.420][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[2024-11-27 20:41:13.423][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:13.426][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:13.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-27 20:41:13.428][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:13.429][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-27 20:41:13.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:13.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:13.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:13.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:13.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:13.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:13.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:13.441][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:13.443][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:13.445][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-27 20:41:13.446][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:13.447][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-27 20:41:13.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:13.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:13.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:13.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:13.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:13.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:13.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:13.458][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:13.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:13.462][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:13.463][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:13.803][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:14.154][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:14.158][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-11-27 20:41:14.166][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-11-27 20:41:14.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:14.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:14.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:14.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:14.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:14.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:14.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:41:14.200][biodb::testThat]
biodb.INFO [2024-11-27 20:41:14.201][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-11-27 20:41:14.202][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:14.203][biodb::testThat]
biodb.DEBUG[2024-11-27 20:41:14.206][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:14.210][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:14.211][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:14.213][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:14.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:14.905][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:14.910][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-11-27 20:41:14.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-11-27 20:41:14.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:14.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:14.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:14.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:14.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:14.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:14.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:14.949][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:14.955][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:14.956][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:14.959][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:15.314][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:15.658][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:15.662][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-11-27 20:41:15.670][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-11-27 20:41:15.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:15.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:15.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:15.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:15.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:15.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.693][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.INFO [2024-11-27 20:41:15.703][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-27 20:41:15.705][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-27 20:41:15.707][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-27 20:41:15.709][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-27 20:41:15.710][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:15.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:15.713][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:15.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:15.716][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:41:15.722][biodb::testContext]
biodb.INFO [2024-11-27 20:41:15.723][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:41:15.725][biodb::testContext] Test context - Test web services
biodb.INFO [2024-11-27 20:41:15.726][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:41:15.727][biodb::testContext]
biodb.INFO [2024-11-27 20:41:15.730][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:41:15.732][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-27 20:41:15.737][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:15.738][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-27 20:41:15.739][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-27 20:41:15.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.743][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-27 20:41:15.744][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-27 20:41:15.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.748][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-27 20:41:15.749][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-27 20:41:15.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.752][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-27 20:41:15.753][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-27 20:41:15.755][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-27 20:41:15.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.758][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-27 20:41:15.759][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-27 20:41:15.760][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-27 20:41:15.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.764][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-27 20:41:15.765][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-27 20:41:15.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.769][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-27 20:41:15.770][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-27 20:41:15.771][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-27 20:41:15.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.774][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-27 20:41:15.775][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-27 20:41:15.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.778][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.DEBUG[2024-11-27 20:41:15.779][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-27 20:41:15.780][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-27 20:41:15.781][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-27 20:41:15.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.785][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:41:15.786][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-27 20:41:15.787][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-27 20:41:15.788][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-27 20:41:15.789][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-27 20:41:15.790][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-27 20:41:15.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.793][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-27 20:41:15.794][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-27 20:41:15.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.798][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-27 20:41:15.799][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-27 20:41:15.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.803][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-27 20:41:15.804][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-27 20:41:15.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.807][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-27 20:41:15.808][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-27 20:41:15.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.812][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-27 20:41:15.813][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-27 20:41:15.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.817][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:41:15.818][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-27 20:41:15.823][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-27 20:41:15.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.826][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-27 20:41:15.827][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-27 20:41:15.828][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-27 20:41:15.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.832][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-27 20:41:15.834][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.835][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-27 20:41:15.836][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.837][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:15.838][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.839][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.840][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.841][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.842][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:41:15.843][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:15.844][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.845][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-27 20:41:15.846][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:15.847][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.848][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.849][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:15.849][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:15.849][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:15.849][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:41:15.849][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:41:15.850][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:15.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:15.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:15.853][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:15.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:15.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:15.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.857][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.858][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:15.859][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:15.860][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.861][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.862][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-27 20:41:15.864][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.865][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:41:15.866][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.867][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:15.868][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.869][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.870][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.871][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.872][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:41:15.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:15.874][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.875][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-27 20:41:15.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:15.877][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.878][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.879][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:15.879][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:15.879][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:15.879][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:41:15.879][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:41:15.880][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:15.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:15.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:15.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:15.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:15.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:15.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.887][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:15.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:15.890][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.891][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.892][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-27 20:41:15.894][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.912][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-27 20:41:15.913][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.914][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:15.915][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.916][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.917][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.918][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.919][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:41:15.920][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:15.921][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.922][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-27 20:41:15.923][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:15.924][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.926][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.927][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:15.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:15.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:15.930][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:15.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:15.932][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:15.932][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.933][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.934][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:15.935][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:15.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.937][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.938][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-27 20:41:15.940][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.941][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:41:15.942][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.943][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:15.944][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.945][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.946][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.947][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.948][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:41:15.949][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:15.950][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.951][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-27 20:41:15.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:15.953][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.954][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:15.955][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:15.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:15.957][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:15.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:15.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:15.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:15.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:15.974][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.975][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:15.976][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:15.977][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:15.978][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:15.980][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:15.981][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:15.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:15.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:15.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:15.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:15.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:15.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:15.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:15.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:15.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:15.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.020][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.DEBUG[2024-11-27 20:41:16.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.041][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[2024-11-27 20:41:16.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.046][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[2024-11-27 20:41:16.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.051][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[2024-11-27 20:41:16.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.066][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-27 20:41:16.068][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-27 20:41:16.069][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-27 20:41:16.071][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-27 20:41:16.072][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:41:16.074][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-27 20:41:16.075][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-27 20:41:16.077][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-27 20:41:16.078][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-27 20:41:16.080][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-27 20:41:16.081][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:41:16.082][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-27 20:41:16.084][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-27 20:41:16.085][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-27 20:41:16.087][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-27 20:41:16.088][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-27 20:41:16.090][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-27 20:41:16.091][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-27 20:41:16.093][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:41:16.094][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-27 20:41:16.096][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-27 20:41:16.097][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-27 20:41:16.098][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-27 20:41:16.100][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-27 20:41:16.101][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-27 20:41:16.103][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-27 20:41:16.104][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-27 20:41:16.106][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-27 20:41:16.107][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-27 20:41:16.109][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-27 20:41:16.110][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-27 20:41:16.112][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-27 20:41:16.113][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-27 20:41:16.114][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-27 20:41:16.116][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-27 20:41:16.117][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-27 20:41:16.119][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-27 20:41:16.120][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-27 20:41:16.122][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-27 20:41:16.123][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-27 20:41:16.125][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-27 20:41:16.126][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-27 20:41:16.128][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-27 20:41:16.129][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-27 20:41:16.131][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-27 20:41:16.132][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-27 20:41:16.133][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-27 20:41:16.135][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-27 20:41:16.136][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-27 20:41:16.138][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-27 20:41:16.139][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-27 20:41:16.141][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-27 20:41:16.142][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-27 20:41:16.144][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-27 20:41:16.145][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-27 20:41:16.147][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-27 20:41:16.148][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-27 20:41:16.150][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-27 20:41:16.151][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-27 20:41:16.153][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-27 20:41:16.154][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-27 20:41:16.156][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-27 20:41:16.157][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-27 20:41:16.158][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-27 20:41:16.160][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-27 20:41:16.161][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-27 20:41:16.163][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:41:16.164][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:41:16.166][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-27 20:41:16.167][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-27 20:41:16.169][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-27 20:41:16.170][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-27 20:41:16.171][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-27 20:41:16.173][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-27 20:41:16.174][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-27 20:41:16.176][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-27 20:41:16.177][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-27 20:41:16.179][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-27 20:41:16.180][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-27 20:41:16.182][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-27 20:41:16.183][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-27 20:41:16.184][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-27 20:41:16.186][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-27 20:41:16.187][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-27 20:41:16.189][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:41:16.191][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:16.191][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.193][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.194][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[2024-11-27 20:41:16.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.312][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[2024-11-27 20:41:16.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.324][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[2024-11-27 20:41:16.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:16.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:16.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:16.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:16.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:16.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:16.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:16.332][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-27 20:41:16.333][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-27 20:41:16.335][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:16.337][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-27 20:41:16.338][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:16.339][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:16.340][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:16.341][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:16.342][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:16.343][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-27 20:41:16.344][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-27 20:41:16.345][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:16.346][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:16.346][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-27 20:41:16.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-27 20:41:16.348][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-27 20:41:16.349][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:16.350][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:16.350][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:16.350][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:16.351][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-27 20:41:16.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:16.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:16.354][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:16.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:16.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:16.357][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:16.357][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:41:16.357][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-27 20:41:16.358][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:16.359][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:16.360][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:16.361][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-27 20:41:16.361][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-27 20:41:16.362][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:41:16.364][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:41:16.365][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-27 20:41:16.367][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:41:16.368][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:41:16.369][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:41:16.373][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-27 20:41:16.374][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-27 20:41:16.375][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-27 20:41:16.376][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-27 20:41:16.377][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:41:16.378][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:41:16.379][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-27 20:41:16.380][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-27 20:41:16.382][biodb::testThat]
biodb.INFO [2024-11-27 20:41:16.383][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-11-27 20:41:16.383][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:16.384][biodb::testThat]
biodb.DEBUG[2024-11-27 20:41:16.387][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-27 20:41:16.391][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:16.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-27 20:41:16.393][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:16.395][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-27 20:41:16.398][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:16.401][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:16.402][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:16.404][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:41:16.745][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:41:17.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:17.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-11-27 20:41:17.105][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-11-27 20:41:17.120][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-27 20:41:17.122][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-27 20:41:17.124][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-27 20:41:17.126][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-27 20:41:17.128][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.131][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.134][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:41:17.142][biodb::testContext]
biodb.INFO [2024-11-27 20:41:17.143][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:41:17.145][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-11-27 20:41:17.146][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:41:17.148][biodb::testContext]
biodb.INFO [2024-11-27 20:41:17.151][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:41:17.153][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-27 20:41:17.158][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:17.159][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-27 20:41:17.161][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-27 20:41:17.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.164][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[2024-11-27 20:41:17.165][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-27 20:41:17.166][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-27 20:41:17.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.170][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-27 20:41:17.171][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-27 20:41:17.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.175][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-27 20:41:17.176][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-27 20:41:17.178][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-27 20:41:17.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.181][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-27 20:41:17.182][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-27 20:41:17.184][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-27 20:41:17.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.187][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-27 20:41:17.188][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-27 20:41:17.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.192][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-27 20:41:17.193][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-27 20:41:17.194][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-27 20:41:17.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.198][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-27 20:41:17.199][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-27 20:41:17.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.203][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-27 20:41:17.204][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-27 20:41:17.205][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-27 20:41:17.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.208][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.DEBUG[2024-11-27 20:41:17.209][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:41:17.210][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-27 20:41:17.211][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-27 20:41:17.212][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-27 20:41:17.213][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-27 20:41:17.214][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-27 20:41:17.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.218][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-27 20:41:17.219][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-27 20:41:17.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.223][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-27 20:41:17.224][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-27 20:41:17.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.228][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-27 20:41:17.229][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-27 20:41:17.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.233][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-27 20:41:17.234][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-27 20:41:17.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.238][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-27 20:41:17.239][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-27 20:41:17.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.242][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:41:17.243][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-27 20:41:17.246][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-27 20:41:17.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.250][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-27 20:41:17.251][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-27 20:41:17.252][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-27 20:41:17.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.256][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-27 20:41:17.258][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.259][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-27 20:41:17.260][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.261][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:17.262][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.264][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.265][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.267][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:41:17.268][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:17.269][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.270][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-27 20:41:17.271][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:17.272][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.273][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.274][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:17.274][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:17.274][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:17.274][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:41:17.274][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:41:17.275][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:17.276][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.278][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:17.279][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.281][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.282][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.283][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:17.284][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:17.285][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.286][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.288][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-27 20:41:17.290][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.291][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:41:17.292][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.293][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:17.294][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.295][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.296][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.297][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.298][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:41:17.299][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:17.300][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.301][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-27 20:41:17.302][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:17.303][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.304][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.305][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:17.305][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:17.305][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:17.305][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:41:17.305][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:41:17.306][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:17.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:17.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.312][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.313][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.314][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:17.315][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:17.316][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.317][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.319][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-27 20:41:17.321][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.322][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-27 20:41:17.323][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:17.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.326][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.327][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.328][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.329][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:41:17.330][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:17.331][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.332][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-27 20:41:17.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:17.334][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.335][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.336][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:17.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:17.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.343][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.343][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.344][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:17.345][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:17.346][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.347][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.349][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-27 20:41:17.350][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.351][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:41:17.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:17.354][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.355][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.356][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.357][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.358][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:41:17.359][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:17.360][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.372][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-27 20:41:17.374][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:17.375][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.375][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.376][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.377][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:41:17.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.380][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:17.381][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.383][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.384][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:17.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:17.387][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.388][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:41:17.389][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:17.390][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.391][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[2024-11-27 20:41:17.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.404][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[2024-11-27 20:41:17.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.409][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[2024-11-27 20:41:17.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.467][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.DEBUG[2024-11-27 20:41:17.468][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-27 20:41:17.469][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-27 20:41:17.471][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-27 20:41:17.472][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-27 20:41:17.474][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:41:17.475][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-27 20:41:17.477][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-27 20:41:17.478][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-27 20:41:17.480][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-27 20:41:17.481][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-27 20:41:17.483][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:41:17.484][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-27 20:41:17.485][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-27 20:41:17.487][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-27 20:41:17.488][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-27 20:41:17.490][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-27 20:41:17.491][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-27 20:41:17.493][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-27 20:41:17.494][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:41:17.495][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-27 20:41:17.497][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-27 20:41:17.498][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-27 20:41:17.500][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-27 20:41:17.501][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-27 20:41:17.503][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-27 20:41:17.504][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-27 20:41:17.506][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-27 20:41:17.507][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-27 20:41:17.508][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-27 20:41:17.510][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-27 20:41:17.511][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-27 20:41:17.513][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-27 20:41:17.514][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-27 20:41:17.516][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-27 20:41:17.517][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-27 20:41:17.518][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-27 20:41:17.520][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-27 20:41:17.521][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-27 20:41:17.523][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-27 20:41:17.524][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-27 20:41:17.526][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-27 20:41:17.527][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-27 20:41:17.528][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-27 20:41:17.530][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-27 20:41:17.531][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-27 20:41:17.533][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-27 20:41:17.534][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-27 20:41:17.536][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-27 20:41:17.537][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-27 20:41:17.539][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-27 20:41:17.540][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-27 20:41:17.542][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-27 20:41:17.543][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-27 20:41:17.544][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-27 20:41:17.546][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-27 20:41:17.547][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-27 20:41:17.549][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-27 20:41:17.550][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-27 20:41:17.552][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-27 20:41:17.553][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-27 20:41:17.555][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-27 20:41:17.556][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-27 20:41:17.557][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-27 20:41:17.559][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-27 20:41:17.560][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-27 20:41:17.562][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-27 20:41:17.563][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:41:17.564][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:41:17.566][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-27 20:41:17.567][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-27 20:41:17.569][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-27 20:41:17.570][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-27 20:41:17.572][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-27 20:41:17.573][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-27 20:41:17.575][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-27 20:41:17.576][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-27 20:41:17.577][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-27 20:41:17.579][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-27 20:41:17.580][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-27 20:41:17.582][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-27 20:41:17.583][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-27 20:41:17.585][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-27 20:41:17.586][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-27 20:41:17.588][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-27 20:41:17.589][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:41:17.590][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:41:17.591][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.593][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.607][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.DEBUG[2024-11-27 20:41:17.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.646][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[2024-11-27 20:41:17.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.665][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[2024-11-27 20:41:17.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.684][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[2024-11-27 20:41:17.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:41:17.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.704][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-27 20:41:17.706][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-27 20:41:17.715][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.716][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.717][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.717][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:41:17.718][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.719][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.720][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.721][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-27 20:41:17.722][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-27 20:41:17.723][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:41:17.724][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.725][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-27 20:41:17.726][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-27 20:41:17.727][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-27 20:41:17.729][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-27 20:41:17.730][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:41:17.730][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:41:17.730][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:41:17.731][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-27 20:41:17.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.734][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:41:17.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:41:17.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:41:17.736][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:41:17.737][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:41:17.737][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-27 20:41:17.738][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:41:17.739][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:41:17.740][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-27 20:41:17.741][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-27 20:41:17.741][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-27 20:41:17.743][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:41:17.744][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:41:17.746][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-27 20:41:17.747][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:41:17.749][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:41:17.750][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:41:17.754][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-27 20:41:17.755][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-27 20:41:17.756][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-27 20:41:17.757][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-27 20:41:17.759][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:41:17.760][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:41:17.761][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-27 20:41:17.762][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-27 20:41:17.763][biodb::testThat]
biodb.INFO [2024-11-27 20:41:17.764][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-11-27 20:41:17.765][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:41:17.766][biodb::testThat]
biodb.DEBUG[2024-11-27 20:41:17.769][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-27 20:41:17.773][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:17.774][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-27 20:41:17.776][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:17.777][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-27 20:41:17.781][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:41:17.784][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:41:17.785][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-27 20:41:17.787][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:41:17.788][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-11-27 20:41:17.805][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-11-27 20:41:17.806][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:41:17.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-11-27 20:41:17.809][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:41:17.810][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:41:17.811][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:41:17.812][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:41:17.813][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:41:17.814][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:41:17.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:17.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:17.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:17.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:17.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:17.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:17.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:41:17.828][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-11-27 20:41:17.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:41:17.831][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:41:17.833][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-11-27 20:41:18.190][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-11-27 20:41:19.177][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:41:19.180][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-11-27 20:41:19.184][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-11-27 20:41:19.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-11-27 20:41:19.188][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:41:19.189][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:41:19.191][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:41:19.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:41:19.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:19.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:19.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:19.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:19.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:19.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:41:19.207][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.208][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.210][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.216][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:41:19.217][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:41:19.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.219][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.220][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:41:19.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:41:19.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.224][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:41:19.226][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:41:19.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.227][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:41:19.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:41:19.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.233][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:41:19.234][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:41:19.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.236][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.238][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:41:19.239][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:41:19.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.241][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.242][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:19.243][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:19.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.245][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.247][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:19.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:41:19.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.251][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:41:19.252][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:19.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.254][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.255][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:41:19.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:41:19.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.260][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:19.261][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:19.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.263][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:19.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:41:19.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.269][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:19.270][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:19.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.272][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:41:19.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:41:19.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.278][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:41:19.279][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:41:19.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.281][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:41:19.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:41:19.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.287][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:41:19.288][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:41:19.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.290][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.291][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:41:19.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:41:19.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:19.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:19.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:19.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:19.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:41:19.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:41:19.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:41:19.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:41:19.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:41:19.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:41:19.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:41:19.337][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-11-27 20:41:19.341][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-27 20:41:19.342][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-27 20:41:19.343][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-27 20:41:19.344][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-27 20:41:19.345][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:41:19.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:41:19.347][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:41:19.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:41:19.348][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:41:19.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
21.395 1.543 52.282
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.950 | 0.125 | 2.170 | |
| ChebiEntry | 0.143 | 0.004 | 0.145 | |