Pierrick Roger
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodbChebi |
| Version: 1.12.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.12.0.tar.gz |
| StartedAt: 2024-11-20 05:36:04 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 05:40:17 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 253.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 1.221 0.065 5.523
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2024-11-20 05:38:14.459][biodb::testContext]
biodb.INFO [2024-11-20 05:38:14.466][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-20 05:38:14.467][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-11-20 05:38:14.469][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-20 05:38:14.470][biodb::testContext]
biodb.INFO [2024-11-20 05:38:14.544][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-20 05:38:14.576][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-20 05:38:14.697][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:38:14.699][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-20 05:38:14.700][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-20 05:38:14.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.706][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-20 05:38:14.735][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-20 05:38:14.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.741][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-20 05:38:14.743][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-20 05:38:14.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.748][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-20 05:38:14.750][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-20 05:38:14.752][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-20 05:38:14.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.757][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-20 05:38:14.759][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-20 05:38:14.760][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-20 05:38:14.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.766][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-20 05:38:14.767][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-20 05:38:14.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.773][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-20 05:38:14.774][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-20 05:38:14.776][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-20 05:38:14.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.782][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-20 05:38:14.783][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-20 05:38:14.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.789][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-20 05:38:14.791][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-20 05:38:14.792][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-20 05:38:14.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.798][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-20 05:38:14.800][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-20 05:38:14.801][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-20 05:38:14.803][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-20 05:38:14.804][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-20 05:38:14.806][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-20 05:38:14.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.811][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[2024-11-20 05:38:14.812][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-20 05:38:14.814][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-20 05:38:14.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.819][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-20 05:38:14.821][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-20 05:38:14.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.825][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[2024-11-20 05:38:14.826][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-20 05:38:14.828][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-20 05:38:14.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.833][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-20 05:38:14.835][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-20 05:38:14.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.840][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-20 05:38:14.842][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-20 05:38:14.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:14.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:14.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:14.848][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-20 05:38:14.849][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-20 05:38:16.711][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-20 05:38:16.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:16.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:16.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:16.761][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-20 05:38:16.763][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-20 05:38:16.765][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-20 05:38:16.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:16.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:16.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:16.776][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-20 05:38:16.843][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:16.913][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-20 05:38:16.915][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:16.916][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:38:16.918][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:16.920][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:38:16.921][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:16.929][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:38:16.931][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-20 05:38:16.933][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:38:16.935][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:16.937][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-20 05:38:16.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:38:16.940][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:16.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:16.944][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:38:16.944][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:38:16.944][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:38:16.944][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-20 05:38:16.944][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-20 05:38:16.946][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:38:16.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:16.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:16.952][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:38:16.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:16.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:16.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:38:16.959][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:16.961][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:38:16.962][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:38:16.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:16.968][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:16.971][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-20 05:38:16.991][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.000][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-20 05:38:17.003][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.005][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:38:17.007][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.009][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.011][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.026][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-20 05:38:17.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:38:17.030][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.032][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-20 05:38:17.040][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:38:17.042][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.045][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.048][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:38:17.048][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:38:17.048][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:38:17.048][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-20 05:38:17.048][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-20 05:38:17.050][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:38:17.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:17.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:17.056][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:38:17.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:17.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:17.061][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.063][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.065][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:38:17.067][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:38:17.069][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.072][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.075][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-20 05:38:17.078][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.081][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-20 05:38:17.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.085][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:38:17.087][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.089][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.091][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.093][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.096][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-20 05:38:17.098][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:38:17.100][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.101][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-20 05:38:17.103][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:38:17.105][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.107][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.109][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.111][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:38:17.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:17.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:17.116][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:38:17.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:17.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:17.125][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.126][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:38:17.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:38:17.132][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.134][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.136][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-20 05:38:17.140][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.142][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-20 05:38:17.143][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.145][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:38:17.146][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.148][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.149][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.151][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.152][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-20 05:38:17.154][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:38:17.155][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.157][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-20 05:38:17.158][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:38:17.160][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.162][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:17.164][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:38:17.167][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:17.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:17.173][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:38:17.174][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:17.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:17.185][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:38:17.187][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.188][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:38:17.189][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:38:17.191][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:17.193][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:38:17.208][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:38:17.218][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.220][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[2024-11-20 05:38:17.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:17.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.233][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[2024-11-20 05:38:17.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:17.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:17.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:17.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:17.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.264][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[2024-11-20 05:38:17.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:17.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:17.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:17.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:17.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:17.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:17.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:17.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:21.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:21.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:21.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:21.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:21.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:21.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:21.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:21.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:21.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:21.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:21.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:21.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:21.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:21.533][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[2024-11-20 05:38:21.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:21.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:21.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:21.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:21.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:21.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:21.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:21.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:21.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:21.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:21.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:22.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:22.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:22.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:22.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:22.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:22.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:22.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:22.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:22.762][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[2024-11-20 05:38:22.764][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-20 05:38:22.783][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-20 05:38:22.788][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-20 05:38:22.793][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-20 05:38:22.795][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-20 05:38:22.800][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-20 05:38:22.808][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-20 05:38:22.815][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-20 05:38:22.824][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-20 05:38:22.826][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-20 05:38:22.831][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-20 05:38:22.839][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-20 05:38:22.842][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-20 05:38:22.844][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-20 05:38:22.846][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-20 05:38:22.848][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-20 05:38:22.857][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-20 05:38:22.862][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-20 05:38:22.864][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-20 05:38:22.866][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-20 05:38:22.869][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-20 05:38:22.871][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-20 05:38:22.873][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-20 05:38:22.876][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-20 05:38:22.878][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-20 05:38:22.881][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-20 05:38:22.884][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-20 05:38:22.888][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-20 05:38:22.890][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-20 05:38:22.901][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-20 05:38:22.903][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-20 05:38:22.906][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-20 05:38:22.908][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-20 05:38:22.910][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-20 05:38:22.912][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-20 05:38:22.914][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-20 05:38:22.916][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-20 05:38:22.933][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-20 05:38:22.935][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-20 05:38:22.937][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-20 05:38:22.939][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-20 05:38:22.942][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-20 05:38:22.947][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-20 05:38:22.950][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-20 05:38:22.952][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-20 05:38:22.955][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-20 05:38:22.957][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-20 05:38:22.960][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-20 05:38:22.962][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-20 05:38:22.964][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-20 05:38:22.967][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-20 05:38:22.969][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-20 05:38:22.971][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-20 05:38:22.973][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-20 05:38:22.976][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-20 05:38:22.978][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-20 05:38:22.980][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-20 05:38:22.983][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-20 05:38:22.985][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-20 05:38:22.988][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-20 05:38:22.990][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-20 05:38:23.009][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-20 05:38:23.012][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-20 05:38:23.014][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-20 05:38:23.016][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-20 05:38:23.018][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-20 05:38:23.020][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-20 05:38:23.022][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-20 05:38:23.024][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-20 05:38:23.027][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-20 05:38:23.029][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-20 05:38:23.031][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-20 05:38:23.033][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-20 05:38:23.035][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-20 05:38:23.037][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-20 05:38:23.040][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-20 05:38:23.042][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-20 05:38:23.044][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-20 05:38:23.046][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-20 05:38:23.048][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-20 05:38:23.050][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-20 05:38:23.052][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-20 05:38:23.055][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-20 05:38:24.458][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-20 05:38:24.516][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-20 05:38:24.523][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:38:24.525][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.528][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.576][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[2024-11-20 05:38:24.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.605][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[2024-11-20 05:38:24.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.624][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[2024-11-20 05:38:24.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.633][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[2024-11-20 05:38:24.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.652][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[2024-11-20 05:38:24.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.672][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[2024-11-20 05:38:24.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:38:24.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:24.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:24.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:24.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:24.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:24.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:38:24.851][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-20 05:38:29.450][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-20 05:38:29.480][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:29.482][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-20 05:38:29.484][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:29.486][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:38:29.487][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:29.489][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:38:29.490][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:29.492][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-20 05:38:29.493][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-20 05:38:29.495][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:38:29.497][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:29.498][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-20 05:38:29.500][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-20 05:38:29.501][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-20 05:38:29.503][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-20 05:38:29.504][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:38:29.504][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:38:29.504][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:38:29.506][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-20 05:38:29.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:29.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:29.510][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:38:29.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:38:29.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:38:29.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:38:29.518][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:38:29.518][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-20 05:38:29.519][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:38:29.521][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:38:29.522][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-20 05:38:29.523][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-20 05:38:29.523][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-20 05:38:29.533][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-20 05:38:29.536][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-20 05:38:29.539][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-20 05:38:29.541][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-20 05:38:29.544][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-20 05:38:29.546][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-20 05:38:29.647][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-20 05:38:29.659][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-20 05:38:29.666][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-20 05:38:29.685][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-20 05:38:29.691][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-20 05:38:29.692][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-20 05:38:29.695][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-20 05:38:29.713][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-20 05:38:29.771][biodb::testThat]
biodb.INFO [2024-11-20 05:38:29.773][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-11-20 05:38:29.775][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:38:29.776][biodb::testThat]
biodb.TRACE[2024-11-20 05:38:29.820][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-11-20 05:38:29.823][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:38:29.828][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:38:29.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:38:29.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:29.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:30.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:30.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:30.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:30.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:38:30.188][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:30.191][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:30.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.195][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:30.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:30.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.244][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:30.245][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:30.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.258][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.310][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:30.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:30.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.316][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:30.318][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:30.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.321][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:30.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:30.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:30.331][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:30.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.334][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:30.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:30.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.342][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:30.344][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:30.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.347][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:30.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:30.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.358][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:30.360][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:30.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.363][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.364][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:30.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:30.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.371][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:38:30.372][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:30.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.396][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.399][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:38:30.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:30.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.405][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:30.414][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:30.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.417][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:30.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:30.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.446][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:38:30.448][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:38:30.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.470][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:38:30.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:38:30.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.501][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:38:30.503][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:38:30.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.506][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.508][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:38:30.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:38:30.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.522][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:38:30.524][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:38:30.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.527][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.529][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:38:30.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:38:30.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:30.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:30.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:30.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:30.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:30.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:30.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:30.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:30.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:30.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:30.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:30.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:30.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:30.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:30.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:30.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:37.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:37.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:37.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:37.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:37.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:37.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:37.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:37.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:37.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:37.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:37.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:37.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:38:37.776][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-11-20 05:38:37.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:37.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:37.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:37.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:37.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:37.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:37.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:37.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:39.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:40.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:40.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:40.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:40.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:40.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:40.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:40.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:40.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:40.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:40.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:40.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:40.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:40.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:40.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:40.524][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-20 05:38:40.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-20 05:38:40.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:40.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:40.530][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-20 05:38:40.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-20 05:38:40.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:40.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:40.536][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-20 05:38:40.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-20 05:38:40.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:40.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:40.542][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-20 05:38:40.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-20 05:38:40.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:40.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:45.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:45.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:45.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:45.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:45.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:45.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:45.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:45.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:45.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:45.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:45.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:45.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:45.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:45.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:45.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:45.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:45.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:45.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:45.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:45.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:45.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:45.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:45.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:45.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:49.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:51.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:51.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:51.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:51.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:51.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:51.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:51.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:51.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:51.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:51.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:51.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:51.446][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:51.447][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:51.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:51.450][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:51.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:51.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:51.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:51.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:51.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:51.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:53.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:54.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:55.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:55.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:55.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:55.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.746][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:55.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:55.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.751][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:38:55.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:38:55.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:38:55.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:38:55.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:38:55.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:38:55.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:38:55.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:38:55.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.834][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:38:55.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:38:55.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.838][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:38:55.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:38:55.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:55.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:55.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:55.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:55.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.935][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:55.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:55.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.941][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:55.942][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:55.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.974][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:55.975][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:55.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:55.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:55.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.083][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.085][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.088][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:56.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.165][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.167][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.170][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:56.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:56.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:56.568][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:58.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:58.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:58.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:58.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.514][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:58.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:58.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.521][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:58.523][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:58.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.526][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.527][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:58.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:58.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.581][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.587][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.589][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.592][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.593][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.612][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.619][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.626][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.632][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.634][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.636][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.638][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.656][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:38:58.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:38:58.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.662][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:38:58.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:38:58.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.692][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:38:58.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:38:58.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.700][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:38:58.701][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:38:58.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.704][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.706][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:38:58.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:38:58.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.747][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.749][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.755][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:58.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:58.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:58.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:58.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:58.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:58.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.801][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:58.802][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:58.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.805][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:58.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:58.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.829][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:58.831][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:58.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.835][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.842][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:58.844][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:58.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.847][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.855][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:58.857][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:58.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.861][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.869][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:58.871][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:58.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.874][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.881][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.883][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:58.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.886][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.893][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.895][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:38:58.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.899][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.906][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:58.908][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:38:58.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.911][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.918][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:58.920][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:38:58.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.923][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.931][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.933][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:38:58.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.936][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.942][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:38:58.944][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:38:58.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.947][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:58.954][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:38:58.955][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:38:58.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:58.958][ef$get] fields variable is a list.
biodb.INFO [2024-11-20 05:38:58.970][biodb::testThat]
biodb.INFO [2024-11-20 05:38:58.972][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-20 05:38:58.974][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:38:58.975][biodb::testThat]
biodb.DEBUG[2024-11-20 05:38:59.061][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-11-20 05:38:59.071][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:38:59.288][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-11-20 05:38:59.327][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:38:59.352][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-11-20 05:38:59.353][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:38:59.421][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:38:59.444][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:38:59.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:38:59.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:38:59.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:38:59.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:38:59.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:38:59.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:38:59.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:38:59.520][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:59.523][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:59.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.526][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:38:59.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:38:59.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.591][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:59.597][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:59.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.600][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.608][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:38:59.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:38:59.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.614][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:59.615][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:59.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.618][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:38:59.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:38:59.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.641][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:59.642][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:59.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.645][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:38:59.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:38:59.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:38:59.670][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:38:59.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:38:59.673][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:38:59.971][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:01.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:01.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.415][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:01.416][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:01.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.419][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.455][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:01.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:01.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.461][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:01.462][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:01.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.465][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.468][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:01.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:01.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.474][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:01.476][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:01.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.478][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:01.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:01.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.487][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:01.489][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:01.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.491][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:01.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:01.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.500][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:01.502][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:01.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.504][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.506][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:01.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:01.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.513][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:01.531][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:01.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.534][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.536][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:01.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:01.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:01.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:01.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:01.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:01.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:01.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:01.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:01.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:01.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:01.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:01.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:01.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:01.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:01.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:01.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:01.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:01.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:01.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:01.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:01.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:01.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:01.666][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-11-20 05:39:01.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-20 05:39:01.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-20 05:39:01.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-20 05:39:01.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-20 05:39:01.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-20 05:39:01.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-20 05:39:01.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-20 05:39:01.728][biodb::testThat]
biodb.INFO [2024-11-20 05:39:01.729][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-20 05:39:01.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:39:01.732][biodb::testThat]
biodb.TRACE[2024-11-20 05:39:01.736][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:01.738][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:01.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.757][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:01.784][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-11-20 05:39:01.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:01.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:01.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:01.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:01.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:01.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:01.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:01.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:01.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:01.921][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-11-20 05:39:01.944][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-20 05:39:02.227][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:39:02.268][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-20 05:39:02.270][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:39:02.295][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-20 05:39:02.423][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[2024-11-20 05:39:02.457][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:39:02.459][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-20 05:39:02.461][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:39:02.483][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-20 05:39:02.486][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-11-20 05:39:02.658][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:02.701][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:02.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:02.705][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:02.706][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:02.708][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:02.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:02.711][ef$get] fields variable is a list.
biodb.INFO [2024-11-20 05:39:02.719][biodb::testThat]
biodb.INFO [2024-11-20 05:39:02.721][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-11-20 05:39:02.722][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:39:02.737][biodb::testThat]
biodb.TRACE[2024-11-20 05:39:02.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:03.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:03.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:03.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:03.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:03.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:03.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:03.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:03.689][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:03.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:03.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:03.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:05.689][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[2024-11-20 05:39:05.794][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:39:05.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-20 05:39:05.798][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:39:05.806][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-11-20 05:39:05.889][biodb::testThat]
biodb.INFO [2024-11-20 05:39:05.891][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-11-20 05:39:05.892][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:39:05.894][biodb::testThat]
biodb.TRACE[2024-11-20 05:39:06.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:06.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:06.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:06.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:06.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:06.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:06.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:06.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:06.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:06.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:06.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:06.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:06.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.080][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-20 05:39:06.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-20 05:39:06.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.086][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-20 05:39:06.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-20 05:39:06.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.093][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-20 05:39:06.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-20 05:39:06.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.116][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-20 05:39:06.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-20 05:39:06.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:06.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:06.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:06.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:06.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:06.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:06.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:06.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:06.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:06.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:06.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:06.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-20 05:39:06.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-20 05:39:06.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-20 05:39:06.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-20 05:39:06.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.194][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-20 05:39:06.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-20 05:39:06.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:06.199][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-20 05:39:06.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-20 05:39:06.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:06.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-20 05:39:06.213][biodb::testThat]
biodb.INFO [2024-11-20 05:39:06.214][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-20 05:39:06.217][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:39:06.218][biodb::testThat]
biodb.INFO [2024-11-20 05:39:06.229][biodb::testThat]
biodb.INFO [2024-11-20 05:39:06.231][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-20 05:39:06.233][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:39:06.234][biodb::testThat]
biodb.INFO [2024-11-20 05:39:06.260][biodb::testThat]
biodb.INFO [2024-11-20 05:39:06.275][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-20 05:39:06.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:39:06.278][biodb::testThat]
biodb.DEBUG[2024-11-20 05:39:06.284][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-11-20 05:39:15.678][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-11-20 05:39:25.695][biodb::testThat]
biodb.INFO [2024-11-20 05:39:25.735][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-20 05:39:25.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:39:25.739][biodb::testThat]
biodb.DEBUG[2024-11-20 05:39:35.310][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[2024-11-20 05:39:37.115][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:37.117][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:37.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.120][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:37.121][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:37.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:37.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.125][ef$get] fields variable is a list.
biodb.INFO [2024-11-20 05:39:37.141][biodb::testThat]
biodb.INFO [2024-11-20 05:39:37.143][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-11-20 05:39:37.144][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:39:37.145][biodb::testThat]
biodb.TRACE[2024-11-20 05:39:37.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:37.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:37.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:37.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:37.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:37.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:37.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:37.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:37.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:37.336][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[2024-11-20 05:39:37.347][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:39:37.349][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-20 05:39:37.351][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:39:37.353][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-20 05:39:37.449][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[2024-11-20 05:39:37.453][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:39:37.455][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-20 05:39:37.457][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:39:37.459][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-11-20 05:39:37.478][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-20 05:39:37.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-20 05:39:37.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:37.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:37.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:37.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:37.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:37.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:37.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:37.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:37.528][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[2024-11-20 05:39:37.532][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:39:37.535][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-20 05:39:37.536][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:39:37.539][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-20 05:39:37.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:37.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:37.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:37.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:37.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:37.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:37.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:37.557][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-11-20 05:39:37.634][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:37.636][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-11-20 05:39:37.638][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:37.639][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:37.641][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:37.642][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:37.643][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:37.645][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:37.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:37.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:37.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:37.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:37.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:37.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:37.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:37.662][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-11-20 05:39:37.666][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:37.668][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:37.669][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-11-20 05:39:38.412][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-11-20 05:39:39.157][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:39.160][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-11-20 05:39:39.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-11-20 05:39:39.217][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-11-20 05:39:39.219][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:39.223][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:39.225][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:39.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:39.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:39.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:39.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:39.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:39.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:39.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:39.252][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.254][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.256][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.264][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:39.266][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:39.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.269][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.271][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:39.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:39.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.277][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:39.279][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:39.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.282][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:39.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:39.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.291][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:39.292][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:39.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.295][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:39.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:39.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.303][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:39.305][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:39.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.308][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:39.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:39.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.316][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:39.317][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:39.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.320][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.322][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:39.324][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.347][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.349][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:39.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.355][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:39.357][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:39.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.360][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:39.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:39.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.368][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:39.369][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:39.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.372][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:39.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:39.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.381][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:39.382][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:39.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.385][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.387][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:39.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:39.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.393][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:39.394][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:39.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.397][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.399][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:39.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:39.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:39.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:39.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:39.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:39.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:39.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:39.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:39.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:39.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:39.464][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-11-20 05:39:39.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:39.497][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[2024-11-20 05:39:39.501][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:39:39.503][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-20 05:39:39.505][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:39:39.508][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-20 05:39:39.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:39.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:39.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:39.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:39.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:39.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:39.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:39.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:39.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:39.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:39.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:39.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:39.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:39.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:39.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:39.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:39.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:39.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:39.574][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-11-20 05:39:39.575][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:39.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-11-20 05:39:39.579][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:39.580][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:39.582][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:39.583][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:39.585][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:39.586][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:39.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:39.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:39.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:39.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:39.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:39.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:39.626][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[2024-11-20 05:39:39.628][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-11-20 05:39:39.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:39.651][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:39.673][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-11-20 05:39:40.415][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-11-20 05:39:41.336][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:41.339][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-11-20 05:39:41.344][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-11-20 05:39:41.347][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-11-20 05:39:41.349][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:41.351][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:41.352][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:41.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:41.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:41.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:41.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:41.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:41.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:41.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:41.370][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.371][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.374][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.381][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:41.382][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:41.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.385][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.386][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:41.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.392][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:41.393][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:41.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.396][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:41.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:41.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.403][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:41.404][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:41.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.407][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:41.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:41.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.414][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:41.415][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:41.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.418][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:41.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:41.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.425][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:41.426][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:41.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.429][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.430][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:41.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.434][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.436][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:41.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.441][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:41.443][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:41.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.445][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:41.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:41.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.452][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:41.454][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:41.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.456][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:41.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:41.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.464][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:41.465][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:41.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.468][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.469][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:41.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:41.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.475][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:41.489][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:41.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.492][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:41.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:41.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:41.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:41.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:41.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:41.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:41.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:41.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:41.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:41.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:41.554][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-11-20 05:39:41.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:41.596][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[2024-11-20 05:39:41.600][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:39:41.602][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-20 05:39:41.604][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:39:41.606][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-20 05:39:41.610][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:41.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:41.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:41.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:41.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:41.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:41.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:41.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:41.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:41.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:41.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:41.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:41.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:41.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:41.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:41.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:41.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:41.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:41.655][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-11-20 05:39:41.656][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:41.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-11-20 05:39:41.660][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:41.661][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:41.663][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:41.664][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:41.665][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:41.667][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:41.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:41.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:41.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:41.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:41.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:41.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:41.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:41.685][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-11-20 05:39:41.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:41.690][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:41.692][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-11-20 05:39:44.293][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-11-20 05:39:45.019][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:45.022][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-11-20 05:39:45.027][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-11-20 05:39:45.031][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-11-20 05:39:45.033][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:45.035][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:45.037][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:45.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:45.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:45.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:45.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:45.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:45.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:45.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:45.055][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.064][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.072][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.080][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:45.082][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:45.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.084][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.086][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:45.088][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:45.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.091][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.093][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:45.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:45.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.097][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.099][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:45.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:45.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.104][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.105][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:45.107][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:45.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.110][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.111][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:45.113][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.116][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.118][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:45.119][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:45.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.122][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.124][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:45.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:45.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.129][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:45.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:45.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.137][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:45.139][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:45.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.141][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:45.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:45.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.149][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:45.151][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:45.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.154][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:45.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:45.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:45.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:45.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:45.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:45.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:45.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:45.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:45.216][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-11-20 05:39:45.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:45.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:45.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:45.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:45.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:45.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:45.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:45.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:45.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:45.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:45.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:45.263][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-11-20 05:39:45.265][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:45.267][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-11-20 05:39:45.269][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:45.271][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:45.272][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:45.274][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:45.275][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:45.277][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:45.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:45.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:45.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:45.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:45.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:45.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:45.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:45.297][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-11-20 05:39:45.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:45.303][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:45.305][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-11-20 05:39:46.052][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-11-20 05:39:48.747][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:48.750][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-11-20 05:39:48.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-11-20 05:39:48.758][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-11-20 05:39:48.760][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:48.761][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:48.763][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:48.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:48.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:48.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:48.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:48.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:48.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:48.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:48.796][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.797][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.800][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.808][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:48.809][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:48.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.812][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.814][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:48.815][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:48.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.818][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.820][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:48.821][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:48.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.824][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.826][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:48.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:48.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.830][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.832][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:48.833][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:48.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.836][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.838][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:48.839][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.842][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.844][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:48.845][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:48.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.848][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.850][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:48.851][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:48.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.854][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:48.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:48.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.862][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:48.864][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:48.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.866][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.868][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:48.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:48.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.874][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:48.875][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:48.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.878][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:48.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:48.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:48.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:48.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:48.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:48.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:48.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:48.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:48.936][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-11-20 05:39:48.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:48.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:48.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:48.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:48.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:48.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:48.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:48.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:48.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:48.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:48.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:48.979][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-11-20 05:39:48.980][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:48.983][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-11-20 05:39:48.984][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:48.986][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:48.987][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:48.989][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:48.990][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:48.992][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:48.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:48.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:48.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:49.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:49.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:49.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:49.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:49.010][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-11-20 05:39:49.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:49.015][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:49.017][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-11-20 05:39:49.755][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-11-20 05:39:50.483][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:50.499][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-11-20 05:39:50.504][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-11-20 05:39:50.508][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-11-20 05:39:50.509][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:50.511][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:50.513][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:50.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:50.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:50.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:50.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:50.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:50.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:50.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:50.532][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.534][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.536][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.544][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:50.545][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:50.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.548][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.550][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:50.551][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:50.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.554][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.556][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:50.558][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:50.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.560][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.562][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:50.564][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:50.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.566][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.568][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:50.570][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:50.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.572][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.574][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:50.575][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.578][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.580][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:50.581][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:50.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.584][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.586][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:50.587][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:50.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.590][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:50.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:50.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.599][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:50.600][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:50.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.603][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.605][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:50.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:50.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.611][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:50.612][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:50.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.615][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:50.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:50.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:50.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:50.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:50.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:50.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:50.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:50.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:50.673][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-11-20 05:39:50.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:50.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:50.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:50.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:50.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:50.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:50.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:50.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:50.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:50.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:50.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:50.715][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-11-20 05:39:50.716][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:50.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-11-20 05:39:50.720][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:50.721][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:50.723][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:50.724][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:50.725][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:50.727][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:50.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:50.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:50.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:50.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:50.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:50.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:50.751][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[2024-11-20 05:39:50.753][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-11-20 05:39:50.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:50.758][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:50.760][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-11-20 05:39:51.519][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-11-20 05:39:52.247][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:52.250][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-11-20 05:39:52.254][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-11-20 05:39:52.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-11-20 05:39:52.261][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:52.263][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:52.264][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:52.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:52.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:52.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:52.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:52.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:52.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:52.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:52.284][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.285][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.288][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.295][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:52.297][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:52.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.299][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.301][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:52.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:52.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.307][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:52.308][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:52.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.310][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:52.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:52.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.318][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:52.320][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:52.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.322][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:52.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:52.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.330][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:52.331][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:52.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.334][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:52.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:52.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.341][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:52.343][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:52.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.345][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.347][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:52.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:52.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.352][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:52.354][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:52.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.356][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.358][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:52.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:52.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.364][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:52.365][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:52.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.368][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:52.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:52.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.375][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:52.376][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:52.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.379][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:52.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:52.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.387][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:52.388][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:52.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.391][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.393][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:52.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:52.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.398][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:52.400][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:52.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.403][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.405][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:52.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:52.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:52.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:52.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:52.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:52.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:52.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:52.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:52.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:52.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:52.479][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-11-20 05:39:52.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:52.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:52.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:52.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:52.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:52.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:52.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:52.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:52.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:52.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:52.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:52.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:52.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:52.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:52.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:52.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:52.538][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-11-20 05:39:52.540][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:52.542][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-11-20 05:39:52.544][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:52.546][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:52.548][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:52.549][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:52.551][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:52.552][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:52.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:52.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:52.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:52.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:52.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:52.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:52.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:52.572][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-11-20 05:39:52.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:52.578][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:52.580][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-11-20 05:39:53.327][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-11-20 05:39:54.054][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:54.057][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-11-20 05:39:54.062][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-11-20 05:39:54.065][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-11-20 05:39:54.067][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:54.069][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:54.071][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:54.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:54.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:54.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:54.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:54.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:54.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:54.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:54.089][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.091][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.093][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.101][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:54.102][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:54.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.105][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.107][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:54.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:54.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.113][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:54.114][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:54.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.117][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.119][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:54.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:54.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.125][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:54.126][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:54.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.129][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:54.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.136][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:54.138][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:54.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.140][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:54.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:54.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.148][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:54.149][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:54.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.152][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.154][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:54.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:54.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.160][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:54.161][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:54.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.164][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.165][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:54.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:54.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.171][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:54.172][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:54.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.175][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:54.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:54.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.182][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:54.183][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:54.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.186][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:54.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:54.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.193][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:54.195][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:54.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.197][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.199][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:54.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:54.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.205][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:54.206][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:54.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.209][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.210][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:54.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:54.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:54.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:54.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:54.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:54.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:54.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:54.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:54.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:54.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:54.283][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-11-20 05:39:54.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:54.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:54.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:54.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:54.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:54.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:54.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:54.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:54.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:54.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:54.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:54.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:54.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:54.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:54.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:54.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:54.314][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-11-20 05:39:54.316][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:54.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-11-20 05:39:54.319][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:54.321][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:54.322][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:54.324][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:54.325][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:54.326][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:54.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:54.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:54.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:54.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:54.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:54.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:54.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:54.344][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-11-20 05:39:54.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:54.349][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:54.351][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-11-20 05:39:55.219][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-11-20 05:39:55.946][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:55.949][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-11-20 05:39:55.954][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-11-20 05:39:55.958][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-11-20 05:39:55.960][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:55.962][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:55.963][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:55.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:55.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:55.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:55.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:55.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:55.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:55.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:55.982][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:55.984][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:55.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:55.987][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:55.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:55.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:55.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:55.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:55.995][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:55.996][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:55.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:55.999][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:56.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:56.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.007][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:56.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:56.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.011][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:56.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:56.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.018][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:56.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:56.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.023][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:56.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:56.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.031][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:56.032][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:56.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.035][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:56.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:56.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.044][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:56.046][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:56.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.049][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.051][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:56.052][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:56.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.055][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.057][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:56.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:56.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.064][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:56.065][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:56.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.068][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:56.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:56.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.076][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:56.078][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:56.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.096][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:56.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:56.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.104][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:56.105][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:56.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.108][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.110][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:56.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:56.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.117][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:56.118][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:56.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.121][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.123][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:56.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:56.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:56.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:56.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:56.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:56.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:56.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:56.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:56.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:56.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:56.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:56.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:56.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:56.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:56.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:56.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:56.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:56.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:56.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:56.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:56.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:56.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:56.183][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-11-20 05:39:56.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:56.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:56.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:56.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:56.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:56.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:56.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:56.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:56.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:56.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:56.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:56.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:56.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:56.214][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[2024-11-20 05:39:56.215][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-11-20 05:39:56.217][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:56.219][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-11-20 05:39:56.221][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:56.222][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:56.224][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:56.225][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:56.227][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:56.228][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:56.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:56.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:56.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:56.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:56.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:56.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:56.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:56.247][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-11-20 05:39:56.251][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:56.252][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:56.254][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-11-20 05:39:57.527][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-11-20 05:39:59.273][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:39:59.276][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-11-20 05:39:59.281][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-11-20 05:39:59.284][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-11-20 05:39:59.286][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:39:59.288][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:39:59.289][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:39:59.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:59.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:59.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:59.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:59.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:59.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:59.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:39:59.308][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.312][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.319][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:59.320][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:59.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.323][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.324][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:39:59.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:39:59.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.330][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:59.331][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:59.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.334][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:39:59.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:39:59.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.341][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:59.343][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:59.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.345][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:39:59.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:39:59.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.366][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:59.367][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:59.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.370][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:39:59.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:39:59.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.377][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:59.378][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:39:59.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.381][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.383][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:59.384][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:59.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.387][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.388][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:39:59.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:59.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.394][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:59.395][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:59.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.398][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:59.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:39:59.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.405][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:59.406][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:59.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.409][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:39:59.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:39:59.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.417][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:59.418][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:59.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.420][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.422][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:39:59.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:39:59.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.428][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:59.429][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:59.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.432][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.433][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:39:59.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:39:59.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:59.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:59.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:59.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:59.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:39:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:39:59.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:39:59.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:39:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:59.493][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-11-20 05:39:59.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:59.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:59.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:59.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:59.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:39:59.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:59.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:39:59.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:39:59.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:39:59.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:59.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:59.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:59.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:59.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:59.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:59.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:59.525][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-11-20 05:39:59.526][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:39:59.528][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-11-20 05:39:59.530][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-20 05:39:59.531][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-20 05:39:59.533][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:39:59.534][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:39:59.535][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-20 05:39:59.537][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-20 05:39:59.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:39:59.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:39:59.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:39:59.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:39:59.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:39:59.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:39:59.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:39:59.555][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-11-20 05:39:59.558][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-20 05:39:59.560][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-20 05:39:59.562][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-11-20 05:40:00.297][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-11-20 05:40:01.680][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-20 05:40:01.684][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-11-20 05:40:01.688][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-11-20 05:40:01.693][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-11-20 05:40:01.695][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-20 05:40:01.697][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:01.698][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:01.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:01.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:01.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:01.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:01.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:01.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:01.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:01.732][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.734][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.737][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.744][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:01.746][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:01.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.749][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.751][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:01.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:01.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.757][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:01.759][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:01.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.761][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.763][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:01.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:01.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.769][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:01.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:01.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.773][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:01.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:01.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.781][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:01.783][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:01.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.785][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:01.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:01.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.793][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:01.794][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:01.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.797][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.799][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:01.800][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:01.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.803][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.805][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:01.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:01.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.811][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:01.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:01.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.815][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:01.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:01.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.823][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:01.824][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:01.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.827][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:01.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:01.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.835][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:01.836][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:01.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.839][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.841][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:01.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:01.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.846][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:01.848][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:01.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.851][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.853][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:01.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:01.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:01.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:01.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:01.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:01.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:01.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:01.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:01.916][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-11-20 05:40:01.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:01.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:01.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:01.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:01.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:01.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:01.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:01.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:01.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:01.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:01.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:01.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:01.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:01.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:01.949][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-11-20 05:40:01.950][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:01.953][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-11-20 05:40:01.954][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:01.957][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml".
biodb.DEBUG[2024-11-20 05:40:01.959][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:01.961][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:01.962][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:01.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:01.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:01.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:01.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:01.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:01.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:01.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:01.990][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.992][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:01.994][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:01.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:01.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:01.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.002][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:02.003][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:02.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.006][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.007][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:02.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:02.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.013][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:02.014][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:02.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.017][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.019][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:02.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:02.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.024][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:02.026][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:02.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.028][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:02.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:02.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.035][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.037][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.039][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.047][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:02.048][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:02.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.051][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.053][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:02.054][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.057][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.059][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:02.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.065][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.067][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.069][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.077][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:02.078][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:02.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.081][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:02.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:02.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.090][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:02.092][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:02.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.095][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.096][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:02.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:02.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.102][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:02.104][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:02.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.107][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.109][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:02.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:02.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:02.169][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-11-20 05:40:02.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:02.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:02.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:02.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:02.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:02.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:02.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:02.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:02.201][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-11-20 05:40:02.202][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:02.205][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-11-20 05:40:02.206][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:02.209][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml".
biodb.DEBUG[2024-11-20 05:40:02.211][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:02.212][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:02.214][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:02.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:02.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:02.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:02.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:02.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:02.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:02.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:02.280][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.282][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.284][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.292][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:02.293][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:02.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.296][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.298][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:02.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:02.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.304][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:02.305][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:02.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.308][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.310][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:02.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:02.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.315][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:02.317][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:02.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:02.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:02.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.328][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.331][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.339][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:02.340][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:02.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.343][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.345][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:02.347][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.349][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.351][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:02.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.358][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.359][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.362][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.371][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:02.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:02.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.375][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:02.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:02.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.384][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:02.386][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:02.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.389][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.391][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:02.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:02.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.397][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:02.399][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:02.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.401][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.403][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:02.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:02.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:02.468][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-11-20 05:40:02.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:02.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:02.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:02.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:02.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:02.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:02.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:02.502][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.DEBUG[2024-11-20 05:40:02.504][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-11-20 05:40:02.506][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:02.508][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-11-20 05:40:02.510][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:02.513][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml".
biodb.DEBUG[2024-11-20 05:40:02.515][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:02.516][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:02.518][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:02.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:02.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:02.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:02.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:02.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:02.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:02.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:02.547][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.549][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.552][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.560][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:02.562][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:02.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.565][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.567][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:02.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:02.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.575][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:02.576][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:02.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.580][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.582][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:02.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:02.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.590][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:02.592][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:02.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.595][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.597][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.599][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.603][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.606][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:02.608][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:02.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.611][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.614][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:02.616][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.619][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.621][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:02.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.629][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.631][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.634][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.644][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:02.646][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:02.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.649][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:02.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:02.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.659][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:02.660][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:02.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.664][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.666][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:02.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:02.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.671][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:02.673][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:02.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.675][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:02.732][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-11-20 05:40:02.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:02.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:02.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:02.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:02.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:02.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:02.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:02.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:02.765][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-11-20 05:40:02.767][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:02.769][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-11-20 05:40:02.771][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:02.773][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2024-11-20 05:40:02.774][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:02.776][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:02.778][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:02.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:02.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:02.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:02.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:02.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:02.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:02.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:02.798][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.799][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.802][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.810][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:02.811][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:02.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.814][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.824][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:02.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:02.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.830][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:02.832][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:02.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.834][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:02.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:02.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.842][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:02.843][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:02.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.846][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.847][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.849][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:02.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.851][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.853][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:02.855][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:02.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.857][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.859][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:02.860][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.863][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.864][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:02.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.870][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.872][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.874][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:02.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.882][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:02.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:02.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.885][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:02.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:02.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.893][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:02.894][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:02.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.897][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.898][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:02.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:02.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.904][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:02.905][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:02.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.908][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:02.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:02.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:02.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:02.962][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-11-20 05:40:02.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:02.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:02.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:02.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:02.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:02.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:02.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:02.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:02.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:02.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:02.992][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[2024-11-20 05:40:02.994][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-11-20 05:40:02.995][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:02.997][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-11-20 05:40:02.999][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:03.002][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2024-11-20 05:40:03.003][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:03.005][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:03.007][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:03.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:03.026][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.027][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.030][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.037][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.038][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.041][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.043][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.048][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:03.050][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:03.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.052][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:03.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:03.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.059][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:03.069][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:03.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.072][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:03.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:03.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.081][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.083][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.091][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:03.092][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:03.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.094][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.096][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:03.098][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.100][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.102][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:03.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.107][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.109][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.111][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.119][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:03.120][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:03.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.122][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.124][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:03.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:03.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.129][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:03.131][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:03.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.133][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.135][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:03.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:03.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.140][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:03.142][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:03.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.144][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.146][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:03.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:03.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:03.204][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-11-20 05:40:03.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:03.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.233][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[2024-11-20 05:40:03.235][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-11-20 05:40:03.236][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:03.238][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-11-20 05:40:03.240][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:03.242][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2024-11-20 05:40:03.244][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:03.245][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:03.247][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:03.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:03.264][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.266][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.268][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.275][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.277][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.279][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.281][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.286][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:03.287][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:03.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.290][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:03.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:03.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.297][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:03.298][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:03.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.309][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:03.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:03.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.317][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.318][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.321][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.328][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:03.329][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:03.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.332][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.333][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:03.335][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.337][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.339][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:03.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.344][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.346][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.348][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.355][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:03.357][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:03.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.359][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:03.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:03.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.367][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:03.368][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:03.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.370][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.372][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:03.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:03.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.377][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:03.379][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:03.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.381][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.383][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:03.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:03.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:03.441][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-11-20 05:40:03.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:03.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:03.472][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-11-20 05:40:03.473][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:03.475][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-11-20 05:40:03.477][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:03.479][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2024-11-20 05:40:03.481][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:03.482][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:03.484][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:03.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:03.501][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.503][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.505][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.512][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.513][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.516][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.518][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.523][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:03.524][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:03.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.527][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:03.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:03.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.534][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:03.535][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:03.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.546][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:03.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:03.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.555][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.558][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.565][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:03.566][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:03.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.569][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.571][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:03.572][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.575][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.576][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:03.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.582][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.586][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.593][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:03.594][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:03.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.597][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:03.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:03.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.604][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:03.605][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:03.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.608][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.610][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:03.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:03.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.616][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:03.617][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:03.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.620][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:03.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:03.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:03.679][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-11-20 05:40:03.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:03.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:03.710][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-11-20 05:40:03.711][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:03.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-11-20 05:40:03.715][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:03.717][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2024-11-20 05:40:03.719][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:03.721][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:03.722][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:03.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:03.740][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.741][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.744][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.751][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.752][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.754][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.756][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.761][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:03.763][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:03.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.765][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:03.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:03.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.772][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:03.774][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:03.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.785][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:03.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:03.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.793][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.795][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.797][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.799][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:03.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.804][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:03.806][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:03.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.808][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.810][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:03.812][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.814][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.816][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:03.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.822][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.823][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.825][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:03.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.833][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:03.834][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:03.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.836][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.838][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:03.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:03.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.844][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:03.845][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:03.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.847][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.849][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:03.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:03.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.854][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:03.856][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:03.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.858][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.860][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:03.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:03.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:03.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:03.918][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-11-20 05:40:03.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:03.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:03.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:03.948][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-11-20 05:40:03.950][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:03.952][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-11-20 05:40:03.953][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:03.956][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2024-11-20 05:40:03.957][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:03.959][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:03.961][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:03.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:03.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:03.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:03.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:03.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:03.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:03.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:03.978][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.980][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.982][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:03.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:03.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.989][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.990][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.993][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:03.994][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:03.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:03.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:03.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.000][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:04.001][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:04.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.003][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.005][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:04.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:04.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.010][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:04.012][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:04.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.014][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:04.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:04.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.031][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.032][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.035][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.042][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:04.043][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:04.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.045][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.047][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:04.048][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.051][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.053][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:04.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.058][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.059][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.062][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.069][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:04.070][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:04.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.072][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:04.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:04.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.080][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:04.081][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:04.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.083][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.085][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:04.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:04.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.090][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:04.092][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:04.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.094][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.096][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:04.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:04.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.153][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-11-20 05:40:04.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:04.183][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-11-20 05:40:04.185][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:04.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-11-20 05:40:04.189][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:04.191][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2024-11-20 05:40:04.192][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:04.194][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:04.196][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:04.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.214][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.215][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.218][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.225][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:04.226][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:04.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.229][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.230][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:04.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:04.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.235][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:04.237][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:04.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.239][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:04.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:04.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.246][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:04.248][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:04.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.250][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:04.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:04.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.267][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.268][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.271][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.278][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:04.279][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:04.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.282][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.284][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:04.285][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.288][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.289][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:04.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.295][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.296][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.299][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.306][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:04.307][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:04.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.310][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:04.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:04.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.317][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:04.319][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:04.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.321][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.323][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:04.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:04.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.328][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:04.330][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:04.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.332][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.334][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:04.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:04.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.394][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-11-20 05:40:04.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:04.425][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-11-20 05:40:04.427][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:04.429][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-11-20 05:40:04.430][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:04.433][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2024-11-20 05:40:04.435][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:04.436][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:04.438][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:04.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.455][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.457][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.459][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.466][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:04.468][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:04.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.470][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.472][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:04.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:04.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.477][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:04.478][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:04.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.481][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:04.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:04.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.488][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:04.489][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:04.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.500][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:04.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:04.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.509][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.510][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:04.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.520][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:04.521][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:04.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.524][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.525][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:04.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.529][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.531][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:04.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.536][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.538][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.540][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:04.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:04.549][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:04.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.551][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:04.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:04.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.558][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:04.560][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:04.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.562][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.564][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:04.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:04.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.569][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:04.571][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:04.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.573][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.575][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:04.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:04.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:04.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:04.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.633][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-11-20 05:40:04.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.674][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[2024-11-20 05:40:04.679][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:04.681][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-20 05:40:04.682][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:04.684][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-20 05:40:04.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.820][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.TRACE[2024-11-20 05:40:04.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:04.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:04.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:04.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:04.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:04.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:04.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:04.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:04.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:04.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:04.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:04.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:05.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.044][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.TRACE[2024-11-20 05:40:05.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.073][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.TRACE[2024-11-20 05:40:05.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.102][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.TRACE[2024-11-20 05:40:05.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.131][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[2024-11-20 05:40:05.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:05.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:05.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:05.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.258][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[2024-11-20 05:40:05.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.288][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[2024-11-20 05:40:05.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.316][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.TRACE[2024-11-20 05:40:05.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.415][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[2024-11-20 05:40:05.419][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:05.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2024-11-20 05:40:05.423][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:05.425][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2024-11-20 05:40:05.429][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[2024-11-20 05:40:05.433][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:05.443][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2024-11-20 05:40:05.446][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:05.449][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2024-11-20 05:40:05.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:05.467][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-11-20 05:40:05.468][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:05.470][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-11-20 05:40:05.472][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:05.475][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2024-11-20 05:40:05.476][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:05.478][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:05.479][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:05.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:05.498][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.499][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.502][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.509][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:05.510][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:05.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.513][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.514][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:05.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:05.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.520][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:05.521][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:05.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.524][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:05.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:05.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.531][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:05.532][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:05.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.535][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:05.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:05.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.542][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:05.543][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:05.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.546][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:05.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:05.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.553][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:05.554][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:05.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.556][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.558][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:05.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:05.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.563][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:05.565][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.567][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.569][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:05.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.574][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.576][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.578][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.585][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:05.587][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:05.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.589][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:05.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:05.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.596][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:05.598][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:05.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.600][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.602][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:05.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:05.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.607][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:05.609][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:05.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.611][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:05.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:05.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.671][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-11-20 05:40:05.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:05.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:05.744][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-11-20 05:40:05.746][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:05.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-11-20 05:40:05.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:05.753][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2024-11-20 05:40:05.754][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:05.756][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:05.758][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:05.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:05.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:05.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:05.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:05.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:05.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:05.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:05.777][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.778][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.781][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.789][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:05.790][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:05.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.793][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.795][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:05.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:05.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.802][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:05.803][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:05.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.806][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:05.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:05.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.814][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:05.816][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:05.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.818][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:05.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:05.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.826][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:05.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:05.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.830][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.832][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:05.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:05.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.837][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:05.839][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:05.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.842][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.844][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:05.845][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.848][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.850][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:05.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:05.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.856][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.857][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.860][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.868][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:05.869][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:05.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.872][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:05.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:05.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.881][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:05.883][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:05.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.886][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.888][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:05.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.894][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:05.896][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:05.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.899][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.901][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:05.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:05.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:05.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:05.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:05.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:05.971][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-11-20 05:40:05.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:05.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:05.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:05.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.012][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[2024-11-20 05:40:06.017][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:06.019][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-20 05:40:06.020][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:06.022][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-20 05:40:06.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.202][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[2024-11-20 05:40:06.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.232][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.TRACE[2024-11-20 05:40:06.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.449][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.TRACE[2024-11-20 05:40:06.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.537][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.TRACE[2024-11-20 05:40:06.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.663][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.TRACE[2024-11-20 05:40:06.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.703][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[2024-11-20 05:40:06.707][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:06.709][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-20 05:40:06.711][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:06.712][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-20 05:40:06.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.757][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.TRACE[2024-11-20 05:40:06.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.838][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.TRACE[2024-11-20 05:40:06.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.878][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.TRACE[2024-11-20 05:40:06.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:06.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:06.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:06.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:06.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:06.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:06.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:06.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:06.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:06.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:06.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.036][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.TRACE[2024-11-20 05:40:07.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.255][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.TRACE[2024-11-20 05:40:07.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.316][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.TRACE[2024-11-20 05:40:07.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.398][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-20 05:40:07.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-20 05:40:07.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-20 05:40:07.413][biodb::testThat]
biodb.INFO [2024-11-20 05:40:07.415][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-11-20 05:40:07.416][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:07.417][biodb::testThat]
biodb.TRACE[2024-11-20 05:40:07.422][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-20 05:40:07.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-20 05:40:07.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:07.469][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[2024-11-20 05:40:07.474][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:07.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-20 05:40:07.478][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:07.479][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-20 05:40:07.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.495][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[2024-11-20 05:40:07.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.514][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[2024-11-20 05:40:07.519][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:07.521][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-20 05:40:07.522][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:07.524][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-20 05:40:07.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:07.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.589][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-20 05:40:07.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.616][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.617][private$selectFields]
biodb.TRACE[2024-11-20 05:40:07.618][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:07.619][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:07.620][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.631][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.633][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.636][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.637][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.639][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.641][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.642][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.644][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.645][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.646][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.649][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.650][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:07.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.681][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-20 05:40:07.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.708][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.710][private$selectFields]
biodb.TRACE[2024-11-20 05:40:07.711][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:07.712][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:07.713][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.719][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.720][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.721][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.724][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.725][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.726][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.728][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.729][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.732][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.733][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:07.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.750][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-20 05:40:07.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:07.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.777][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.778][private$selectFields]
biodb.TRACE[2024-11-20 05:40:07.779][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:07.780][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:07.782][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.783][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.787][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.788][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.790][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.792][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.793][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.795][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:07.796][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.800][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.801][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:07.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:07.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.819][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-20 05:40:07.821][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-20 05:40:07.822][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-20 05:40:07.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:07.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:07.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:07.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:07.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:07.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:07.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:07.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:07.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:07.965][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[2024-11-20 05:40:07.969][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:07.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-20 05:40:07.973][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:07.975][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-20 05:40:07.979][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[2024-11-20 05:40:07.984][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:07.986][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-20 05:40:07.988][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:07.990][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-20 05:40:07.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:07.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:07.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.135][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-20 05:40:08.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.198][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.199][private$selectFields]
biodb.TRACE[2024-11-20 05:40:08.200][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:08.202][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:08.203][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.204][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.208][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.210][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.211][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.213][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.215][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.216][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.217][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.219][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.221][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.223][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:08.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.240][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-20 05:40:08.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.324][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.326][private$selectFields]
biodb.TRACE[2024-11-20 05:40:08.328][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:08.329][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:08.330][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.332][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.333][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.336][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.337][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.339][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.341][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.342][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.358][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.360][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.362][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.364][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.366][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:08.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.384][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-20 05:40:08.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.410][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.411][private$selectFields]
biodb.TRACE[2024-11-20 05:40:08.412][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:08.414][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:08.415][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.416][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.420][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.422][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.423][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.426][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.427][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.428][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.429][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.431][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.433][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.435][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:08.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.452][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-20 05:40:08.454][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-20 05:40:08.455][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-20 05:40:08.466][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-20 05:40:08.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-20 05:40:08.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-20 05:40:08.475][biodb::testThat]
biodb.INFO [2024-11-20 05:40:08.477][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-11-20 05:40:08.478][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:08.479][biodb::testThat]
biodb.TRACE[2024-11-20 05:40:08.483][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-20 05:40:08.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-20 05:40:08.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.526][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[2024-11-20 05:40:08.530][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[2024-11-20 05:40:08.534][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:08.536][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-20 05:40:08.538][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:08.539][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-20 05:40:08.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.583][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[2024-11-20 05:40:08.588][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:08.589][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-20 05:40:08.591][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:08.593][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-20 05:40:08.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.638][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[2024-11-20 05:40:08.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:08.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.656][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-20 05:40:08.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.682][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.683][private$selectFields]
biodb.TRACE[2024-11-20 05:40:08.685][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:08.686][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:08.687][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.688][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.690][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.692][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.693][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.695][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.697][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.699][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.700][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.701][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.703][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.705][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.707][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:08.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.724][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-20 05:40:08.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.750][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.751][private$selectFields]
biodb.TRACE[2024-11-20 05:40:08.752][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:08.754][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:08.755][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.756][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.758][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.760][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.761][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.763][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.765][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.766][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.768][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.769][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.770][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.773][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.774][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:08.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.801][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-20 05:40:08.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.815][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.TRACE[2024-11-20 05:40:08.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.828][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.829][private$selectFields]
biodb.TRACE[2024-11-20 05:40:08.830][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:08.832][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:08.833][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.834][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.836][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.838][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.839][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.841][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.843][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.845][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.846][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:08.847][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.849][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.851][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.852][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:08.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:08.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.870][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-20 05:40:08.871][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-20 05:40:08.872][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-20 05:40:08.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:08.924][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[2024-11-20 05:40:08.928][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:08.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-20 05:40:08.932][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:08.933][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-20 05:40:08.938][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[2024-11-20 05:40:08.942][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:08.944][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-20 05:40:08.946][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:08.948][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-20 05:40:08.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:08.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:08.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:08.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:08.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:08.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:08.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:08.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:08.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:08.993][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[2024-11-20 05:40:08.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:08.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:08.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.051][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-20 05:40:09.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.077][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.079][private$selectFields]
biodb.TRACE[2024-11-20 05:40:09.080][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:09.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:09.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.084][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.085][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.088][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.089][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.090][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.093][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.094][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.096][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.097][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.101][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.102][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:09.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.120][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-20 05:40:09.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.146][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.147][private$selectFields]
biodb.TRACE[2024-11-20 05:40:09.149][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:09.150][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:09.151][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.154][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.156][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.158][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.159][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.162][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.163][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.164][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.165][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.169][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.171][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:09.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.188][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-20 05:40:09.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.202][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[2024-11-20 05:40:09.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.214][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.215][private$selectFields]
biodb.TRACE[2024-11-20 05:40:09.216][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:09.217][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:09.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.220][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.224][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.229][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.230][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.232][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.237][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.238][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:09.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.255][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-20 05:40:09.257][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-20 05:40:09.258][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-20 05:40:09.278][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-20 05:40:09.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-20 05:40:09.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-20 05:40:09.288][biodb::testThat]
biodb.INFO [2024-11-20 05:40:09.289][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-11-20 05:40:09.291][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:09.292][biodb::testThat]
biodb.TRACE[2024-11-20 05:40:09.296][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-20 05:40:09.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-20 05:40:09.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.341][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[2024-11-20 05:40:09.345][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[2024-11-20 05:40:09.349][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:09.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-20 05:40:09.353][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:09.355][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-20 05:40:09.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.388][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[2024-11-20 05:40:09.393][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:09.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-20 05:40:09.396][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:09.398][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-20 05:40:09.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.413][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.TRACE[2024-11-20 05:40:09.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:09.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.460][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-20 05:40:09.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.486][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.488][private$selectFields]
biodb.TRACE[2024-11-20 05:40:09.489][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:09.490][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:09.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.494][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.496][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.498][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.514][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.515][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.516][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.518][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.522][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:09.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.539][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-20 05:40:09.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.565][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.566][private$selectFields]
biodb.TRACE[2024-11-20 05:40:09.567][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:09.568][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:09.570][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.575][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.576][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.578][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.580][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.582][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.583][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.584][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.586][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.588][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.589][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:09.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.607][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-20 05:40:09.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.633][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.634][private$selectFields]
biodb.TRACE[2024-11-20 05:40:09.635][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:09.636][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:09.637][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.639][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.640][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.643][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.644][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.645][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.648][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.649][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.650][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.652][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.653][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.655][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.657][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:09.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.674][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-20 05:40:09.675][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-20 05:40:09.677][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-20 05:40:09.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.751][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[2024-11-20 05:40:09.755][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[2024-11-20 05:40:09.759][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:09.761][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-20 05:40:09.763][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:09.765][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-20 05:40:09.769][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[2024-11-20 05:40:09.773][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:09.775][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-20 05:40:09.776][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:09.778][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-20 05:40:09.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.824][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[2024-11-20 05:40:09.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:09.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:09.871][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-20 05:40:09.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.897][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.899][private$selectFields]
biodb.TRACE[2024-11-20 05:40:09.900][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:09.901][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:09.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.905][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.908][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.909][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.910][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.913][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.914][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.915][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.917][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.918][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.920][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.922][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:09.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.940][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-20 05:40:09.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:09.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:09.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:09.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:09.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:09.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:09.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:09.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.966][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.967][private$selectFields]
biodb.TRACE[2024-11-20 05:40:09.968][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:09.979][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:09.981][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.984][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.986][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.989][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.992][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:09.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.994][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:09.996][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.997][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:09.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:09.999][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.001][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:10.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.019][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-20 05:40:10.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:10.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:10.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:10.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:10.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:10.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:10.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:10.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:10.047][private$selectFields]
biodb.TRACE[2024-11-20 05:40:10.048][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-20 05:40:10.049][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-20 05:40:10.050][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:10.052][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.053][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.056][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.057][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.058][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.061][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.062][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:10.064][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-20 05:40:10.065][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.066][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.069][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.070][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-20 05:40:10.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.088][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-20 05:40:10.089][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-20 05:40:10.090][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-20 05:40:10.116][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-20 05:40:10.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-20 05:40:10.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-20 05:40:10.125][biodb::testThat]
biodb.INFO [2024-11-20 05:40:10.126][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-11-20 05:40:10.128][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:10.129][biodb::testThat]
biodb.DEBUG[2024-11-20 05:40:10.131][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-11-20 05:40:10.133][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:10.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-11-20 05:40:10.136][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:10.139][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2024-11-20 05:40:10.140][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:10.142][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:10.143][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:10.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:10.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:10.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:10.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:10.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:10.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:10.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:10.161][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.162][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.165][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.172][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:10.173][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:10.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.175][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.177][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:10.178][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:10.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.181][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.183][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:10.184][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:10.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.186][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.188][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.189][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.192][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.193][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.195][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.197][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.199][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:10.200][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:10.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.202][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.204][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.215][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.218][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.220][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:10.221][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:10.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.224][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.225][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:10.227][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:10.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.229][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.231][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:10.232][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:10.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.235][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:10.289][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-11-20 05:40:10.290][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-11-20 05:40:10.300][biodb::testThat]
biodb.INFO [2024-11-20 05:40:10.302][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-11-20 05:40:10.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:10.304][biodb::testThat]
biodb.DEBUG[2024-11-20 05:40:10.318][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-11-20 05:40:10.320][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-11-20 05:40:10.321][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-11-20 05:40:10.323][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-11-20 05:40:10.325][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-11-20 05:40:10.329][loadFileContents] Loaded 3 files from cache: [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2024-11-20 05:40:10.330][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:10.332][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-11-20 05:40:10.333][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:10.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:10.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:10.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:10.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:10.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:10.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:10.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:10.351][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.352][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.355][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.362][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:10.363][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:10.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.366][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.367][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:10.369][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:10.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.371][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.373][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:10.375][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:10.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.377][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.379][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.380][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.383][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.384][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.385][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.388][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.390][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:10.391][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:10.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.393][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.395][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.397][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.399][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.401][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:10.402][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:10.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.404][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.406][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:10.408][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:10.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.410][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.412][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:10.413][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:10.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.416][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:10.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:10.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:10.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:10.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:10.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:10.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:10.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:10.480][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.482][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.484][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.491][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:10.493][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:10.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.495][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.497][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:10.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:10.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.508][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:10.510][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:10.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.516][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:10.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:10.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.522][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:10.523][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:10.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.526][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:10.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:10.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.536][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.538][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.542][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.551][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.553][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.557][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.559][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.567][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:10.568][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:10.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.572][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.574][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:10.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:10.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.581][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.587][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.596][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:10.598][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:10.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.602][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:10.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:10.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.612][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:10.614][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:10.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.617][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.620][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:10.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:10.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.627][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:10.629][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:10.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.632][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.635][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:10.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:10.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:10.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:10.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:10.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:10.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:10.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:10.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:10.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:10.704][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.706][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.708][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.716][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:10.718][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:10.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.721][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.723][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:10.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:10.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.747][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:10.749][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:10.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.752][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:10.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:10.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.760][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:10.761][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:10.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.764][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.765][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:10.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:10.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.771][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.773][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.775][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:10.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.783][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.784][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.787][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.788][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:10.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.794][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:10.795][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:10.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.798][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.799][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:10.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:10.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.805][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.806][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.808][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:10.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.815][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:10.816][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:10.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.819][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:10.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:10.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.826][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:10.827][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:10.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.829][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.831][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:10.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:10.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.836][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:10.838][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:10.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.840][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.841][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:10.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:10.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:10.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:10.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:10.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:10.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:10.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:10.927][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-11-20 05:40:10.929][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-11-20 05:40:10.930][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-11-20 05:40:10.947][biodb::testThat]
biodb.INFO [2024-11-20 05:40:10.949][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-11-20 05:40:10.950][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:10.951][biodb::testThat]
biodb.INFO [2024-11-20 05:40:10.996][biodb::testThat]
biodb.INFO [2024-11-20 05:40:10.997][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-11-20 05:40:10.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:11.000][biodb::testThat]
biodb.INFO [2024-11-20 05:40:11.011][biodb::testThat]
biodb.INFO [2024-11-20 05:40:11.012][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-11-20 05:40:11.013][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:11.015][biodb::testThat]
biodb.DEBUG[2024-11-20 05:40:11.018][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[2024-11-20 05:40:11.023][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:11.024][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2024-11-20 05:40:11.026][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:11.029][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2024-11-20 05:40:11.045][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:11.047][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:11.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:11.049][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:11.050][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:11.052][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:11.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:11.054][ef$get] fields variable is a list.
biodb.INFO [2024-11-20 05:40:11.057][biodb::testThat]
biodb.INFO [2024-11-20 05:40:11.058][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-11-20 05:40:11.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:11.060][biodb::testThat]
biodb.ERROR[2024-11-20 05:40:11.080][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-11-20 05:40:11.104][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-11-20 05:40:11.123][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-20 05:40:11.124][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-20 05:40:11.126][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-20 05:40:11.127][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-20 05:40:11.128][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.131][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.133][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-20 05:40:11.150][biodb::testContext]
biodb.INFO [2024-11-20 05:40:11.152][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-20 05:40:11.153][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-11-20 05:40:11.154][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-20 05:40:11.156][biodb::testContext]
biodb.INFO [2024-11-20 05:40:11.158][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-20 05:40:11.161][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-20 05:40:11.167][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:11.168][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-20 05:40:11.170][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-20 05:40:11.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.175][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-20 05:40:11.176][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-20 05:40:11.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.180][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[2024-11-20 05:40:11.182][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-20 05:40:11.183][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-20 05:40:11.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.189][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-20 05:40:11.190][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-20 05:40:11.192][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-20 05:40:11.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.197][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-20 05:40:11.198][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-20 05:40:11.200][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-20 05:40:11.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.205][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-20 05:40:11.206][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-20 05:40:11.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.220][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[2024-11-20 05:40:11.221][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-20 05:40:11.223][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-20 05:40:11.225][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-20 05:40:11.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.230][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-20 05:40:11.231][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-20 05:40:11.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.236][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-20 05:40:11.238][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-20 05:40:11.239][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-20 05:40:11.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.244][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-20 05:40:11.246][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-20 05:40:11.247][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-20 05:40:11.248][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-20 05:40:11.250][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-20 05:40:11.251][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-20 05:40:11.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.255][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[2024-11-20 05:40:11.256][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-20 05:40:11.258][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-20 05:40:11.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.263][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-20 05:40:11.265][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-20 05:40:11.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.270][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-20 05:40:11.271][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-20 05:40:11.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.276][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-20 05:40:11.278][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-20 05:40:11.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.283][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-20 05:40:11.284][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-20 05:40:11.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.290][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-20 05:40:11.291][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-20 05:40:11.296][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-20 05:40:11.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.302][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-20 05:40:11.303][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-20 05:40:11.305][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-20 05:40:11.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.311][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-20 05:40:11.313][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.315][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-20 05:40:11.317][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.318][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:11.320][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.321][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.323][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.324][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.326][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-20 05:40:11.327][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:11.329][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.330][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-20 05:40:11.332][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:11.333][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.335][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.336][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:11.336][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:11.336][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:11.336][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-20 05:40:11.336][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-20 05:40:11.338][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:11.339][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.342][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:11.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.346][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.347][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.349][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:11.350][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:11.352][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.353][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.355][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-20 05:40:11.357][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.359][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-20 05:40:11.360][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.362][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:11.363][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.366][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.368][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.369][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-20 05:40:11.371][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:11.372][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.373][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-20 05:40:11.375][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:11.376][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.378][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.379][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:11.379][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:11.379][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:11.379][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-20 05:40:11.379][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-20 05:40:11.381][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:11.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:11.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.389][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.390][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:11.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:11.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.396][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.398][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-20 05:40:11.400][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.401][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-20 05:40:11.403][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.404][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:11.406][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.407][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.409][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.410][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.411][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-20 05:40:11.413][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:11.414][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.416][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-20 05:40:11.417][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:11.418][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.420][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.421][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.423][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:11.424][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.425][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.427][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:11.428][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.431][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.432][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.434][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:11.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:11.436][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.438][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.439][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-20 05:40:11.442][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.443][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-20 05:40:11.445][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.446][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:11.448][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.449][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.450][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.452][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.453][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-20 05:40:11.463][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:11.465][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.466][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-20 05:40:11.468][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:11.469][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.470][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.472][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.473][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:11.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.477][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:11.478][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.481][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.482][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.484][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:11.485][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:11.486][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.488][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:11.489][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:11.491][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.516][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[2024-11-20 05:40:11.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.528][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[2024-11-20 05:40:11.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.599][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-20 05:40:11.601][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-20 05:40:11.603][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-20 05:40:11.605][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-20 05:40:11.607][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-20 05:40:11.609][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-20 05:40:11.612][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-20 05:40:11.614][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-20 05:40:11.616][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-20 05:40:11.618][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-20 05:40:11.620][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-20 05:40:11.622][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-20 05:40:11.624][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-20 05:40:11.626][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-20 05:40:11.628][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-20 05:40:11.630][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-20 05:40:11.632][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-20 05:40:11.634][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-20 05:40:11.636][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-20 05:40:11.638][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-20 05:40:11.640][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-20 05:40:11.642][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-20 05:40:11.644][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-20 05:40:11.646][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-20 05:40:11.648][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-20 05:40:11.650][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-20 05:40:11.652][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-20 05:40:11.654][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-20 05:40:11.656][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-20 05:40:11.658][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-20 05:40:11.660][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-20 05:40:11.662][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-20 05:40:11.664][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-20 05:40:11.666][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-20 05:40:11.668][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-20 05:40:11.670][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-20 05:40:11.672][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-20 05:40:11.674][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-20 05:40:11.676][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-20 05:40:11.678][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-20 05:40:11.680][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-20 05:40:11.682][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-20 05:40:11.684][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-20 05:40:11.694][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-20 05:40:11.697][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-20 05:40:11.699][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-20 05:40:11.701][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-20 05:40:11.703][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-20 05:40:11.705][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-20 05:40:11.707][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-20 05:40:11.709][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-20 05:40:11.711][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-20 05:40:11.713][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-20 05:40:11.715][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-20 05:40:11.717][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-20 05:40:11.719][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-20 05:40:11.721][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-20 05:40:11.723][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-20 05:40:11.725][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-20 05:40:11.726][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-20 05:40:11.728][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-20 05:40:11.730][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-20 05:40:11.732][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-20 05:40:11.734][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-20 05:40:11.736][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-20 05:40:11.738][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-20 05:40:11.740][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-20 05:40:11.742][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-20 05:40:11.744][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-20 05:40:11.746][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-20 05:40:11.748][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-20 05:40:11.750][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-20 05:40:11.752][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-20 05:40:11.754][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-20 05:40:11.756][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-20 05:40:11.758][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-20 05:40:11.760][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-20 05:40:11.762][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-20 05:40:11.764][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-20 05:40:11.766][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-20 05:40:11.768][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-20 05:40:11.770][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-20 05:40:11.772][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-20 05:40:11.774][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-20 05:40:11.776][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-20 05:40:11.778][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:11.779][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.781][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.792][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[2024-11-20 05:40:11.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.871][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[2024-11-20 05:40:11.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.897][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[2024-11-20 05:40:11.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:11.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:11.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:11.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:11.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:11.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:11.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:11.944][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-20 05:40:11.946][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-20 05:40:11.949][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.950][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.952][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:11.954][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.956][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.957][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.959][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-20 05:40:11.960][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-20 05:40:11.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:11.963][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.964][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-20 05:40:11.965][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-20 05:40:11.967][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-20 05:40:11.968][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:11.970][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:11.970][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:11.970][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:11.971][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-20 05:40:11.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.975][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:11.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:11.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:11.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:11.980][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:40:11.980][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-20 05:40:11.981][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:11.983][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:11.984][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:11.985][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-20 05:40:11.985][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-20 05:40:11.987][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-20 05:40:11.989][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-20 05:40:11.991][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-20 05:40:11.994][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-20 05:40:11.996][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-20 05:40:11.998][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-20 05:40:12.003][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-20 05:40:12.004][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-20 05:40:12.006][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-20 05:40:12.008][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-20 05:40:12.010][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-20 05:40:12.011][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-20 05:40:12.013][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-20 05:40:12.014][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-20 05:40:12.016][biodb::testThat]
biodb.INFO [2024-11-20 05:40:12.018][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-11-20 05:40:12.019][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:12.020][biodb::testThat]
biodb.DEBUG[2024-11-20 05:40:12.025][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-20 05:40:12.030][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.032][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-20 05:40:12.034][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.037][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-20 05:40:12.042][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[2024-11-20 05:40:12.046][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.048][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-20 05:40:12.050][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.052][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-20 05:40:12.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.067][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[2024-11-20 05:40:12.070][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[2024-11-20 05:40:12.075][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.077][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-20 05:40:12.079][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.082][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-20 05:40:12.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.132][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.DEBUG[2024-11-20 05:40:12.138][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[2024-11-20 05:40:12.143][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.145][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-20 05:40:12.146][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.148][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-20 05:40:12.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.174][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[2024-11-20 05:40:12.179][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.180][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-20 05:40:12.182][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.184][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-20 05:40:12.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.218][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[2024-11-20 05:40:12.222][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-20 05:40:12.226][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.228][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-20 05:40:12.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.245][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[2024-11-20 05:40:12.249][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.251][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-20 05:40:12.253][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.254][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-20 05:40:12.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.272][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[2024-11-20 05:40:12.276][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-11-20 05:40:12.280][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.283][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-11-20 05:40:12.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.298][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.INFO [2024-11-20 05:40:12.307][biodb::testThat]
biodb.INFO [2024-11-20 05:40:12.308][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-11-20 05:40:12.310][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:12.311][biodb::testThat]
biodb.DEBUG[2024-11-20 05:40:12.315][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[2024-11-20 05:40:12.320][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.322][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2024-11-20 05:40:12.324][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.326][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2024-11-20 05:40:12.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.341][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[2024-11-20 05:40:12.346][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[2024-11-20 05:40:12.351][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:12.352][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2024-11-20 05:40:12.354][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:12.357][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2024-11-20 05:40:12.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:12.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-20 05:40:12.379][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-20 05:40:12.381][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-20 05:40:12.382][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-20 05:40:12.383][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-20 05:40:12.385][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:12.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:12.387][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.389][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.391][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.INFO [2024-11-20 05:40:12.396][biodb::testContext]
biodb.INFO [2024-11-20 05:40:12.397][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-20 05:40:12.399][biodb::testContext] Test context - Test web services
biodb.INFO [2024-11-20 05:40:12.400][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-20 05:40:12.401][biodb::testContext]
biodb.INFO [2024-11-20 05:40:12.628][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-20 05:40:12.630][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-20 05:40:12.635][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:12.636][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-20 05:40:12.637][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-20 05:40:12.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.642][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-20 05:40:12.644][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-20 05:40:12.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.648][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-20 05:40:12.650][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-20 05:40:12.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.655][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-20 05:40:12.656][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-20 05:40:12.657][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-20 05:40:12.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.662][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-20 05:40:12.663][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-20 05:40:12.665][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-20 05:40:12.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.670][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-20 05:40:12.671][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-20 05:40:12.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.675][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[2024-11-20 05:40:12.676][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-20 05:40:12.677][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-20 05:40:12.679][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-20 05:40:12.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.684][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-20 05:40:12.685][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-20 05:40:12.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.690][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-20 05:40:12.691][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-20 05:40:12.693][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-20 05:40:12.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.697][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-20 05:40:12.699][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-20 05:40:12.700][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-20 05:40:12.701][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-20 05:40:12.703][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-20 05:40:12.704][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-20 05:40:12.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.709][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-20 05:40:12.710][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-20 05:40:12.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.715][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-20 05:40:12.717][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-20 05:40:12.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.721][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-20 05:40:12.723][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-20 05:40:12.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.728][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-20 05:40:12.729][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-20 05:40:12.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.734][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-20 05:40:12.735][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-20 05:40:12.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.740][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-20 05:40:12.742][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-20 05:40:12.747][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-20 05:40:12.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.751][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[2024-11-20 05:40:12.752][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-20 05:40:12.753][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-20 05:40:12.755][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-20 05:40:12.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.760][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-20 05:40:12.762][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.763][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-20 05:40:12.765][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.766][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:12.767][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.769][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.770][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.771][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.773][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-20 05:40:12.774][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:12.775][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.777][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-20 05:40:12.778][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:12.779][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.782][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:12.782][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:12.782][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:12.782][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-20 05:40:12.782][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-20 05:40:12.783][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:12.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:12.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:12.787][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:12.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:12.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:12.791][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.792][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.793][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:12.794][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:12.796][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.797][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.799][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-20 05:40:12.801][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.802][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-20 05:40:12.804][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.805][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:12.807][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.811][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.812][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-20 05:40:12.813][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:12.815][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.816][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-20 05:40:12.817][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:12.819][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.820][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.821][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:12.821][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:12.821][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:12.821][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-20 05:40:12.821][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-20 05:40:12.823][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:12.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:12.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:12.826][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:12.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:12.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:12.830][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.831][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.832][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:12.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:12.835][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.836][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.838][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-20 05:40:12.840][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.842][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-20 05:40:12.843][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.844][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:12.846][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.847][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.848][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.849][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.851][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-20 05:40:12.852][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:12.853][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.855][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-20 05:40:12.863][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:12.865][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.866][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.867][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.869][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:12.870][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:12.871][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:12.872][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:12.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:12.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:12.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.877][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.878][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:12.880][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:12.881][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.882][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.884][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-20 05:40:12.886][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.887][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-20 05:40:12.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.890][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:12.891][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.896][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-20 05:40:12.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:12.899][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.900][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-20 05:40:12.901][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:12.902][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.904][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:12.905][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.906][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:12.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:12.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:12.910][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:12.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:12.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:12.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:12.915][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:12.918][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:12.919][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:12.920][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:12.922][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:12.923][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.942][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[2024-11-20 05:40:12.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.954][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.DEBUG[2024-11-20 05:40:12.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.984][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[2024-11-20 05:40:12.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:12.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:12.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:12.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:12.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:12.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.001][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[2024-11-20 05:40:13.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.026][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-20 05:40:13.028][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-20 05:40:13.030][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-20 05:40:13.032][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-20 05:40:13.033][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-20 05:40:13.035][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-20 05:40:13.037][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-20 05:40:13.039][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-20 05:40:13.041][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-20 05:40:13.043][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-20 05:40:13.045][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-20 05:40:13.047][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-20 05:40:13.049][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-20 05:40:13.050][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-20 05:40:13.052][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-20 05:40:13.054][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-20 05:40:13.056][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-20 05:40:13.058][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-20 05:40:13.060][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-20 05:40:13.062][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-20 05:40:13.064][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-20 05:40:13.066][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-20 05:40:13.068][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-20 05:40:13.069][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-20 05:40:13.071][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-20 05:40:13.073][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-20 05:40:13.075][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-20 05:40:13.077][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-20 05:40:13.079][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-20 05:40:13.081][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-20 05:40:13.089][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-20 05:40:13.091][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-20 05:40:13.093][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-20 05:40:13.095][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-20 05:40:13.097][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-20 05:40:13.099][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-20 05:40:13.101][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-20 05:40:13.103][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-20 05:40:13.104][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-20 05:40:13.106][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-20 05:40:13.108][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-20 05:40:13.110][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-20 05:40:13.112][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-20 05:40:13.114][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-20 05:40:13.116][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-20 05:40:13.117][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-20 05:40:13.119][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-20 05:40:13.121][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-20 05:40:13.123][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-20 05:40:13.125][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-20 05:40:13.127][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-20 05:40:13.129][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-20 05:40:13.130][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-20 05:40:13.132][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-20 05:40:13.134][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-20 05:40:13.136][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-20 05:40:13.138][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-20 05:40:13.140][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-20 05:40:13.142][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-20 05:40:13.144][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-20 05:40:13.146][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-20 05:40:13.148][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-20 05:40:13.150][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-20 05:40:13.151][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-20 05:40:13.153][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-20 05:40:13.155][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-20 05:40:13.157][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-20 05:40:13.159][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-20 05:40:13.161][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-20 05:40:13.163][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-20 05:40:13.165][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-20 05:40:13.167][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-20 05:40:13.169][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-20 05:40:13.171][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-20 05:40:13.172][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-20 05:40:13.174][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-20 05:40:13.176][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-20 05:40:13.178][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-20 05:40:13.180][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-20 05:40:13.182][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-20 05:40:13.184][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-20 05:40:13.186][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-20 05:40:13.188][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-20 05:40:13.190][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-20 05:40:13.192][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-20 05:40:13.193][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:13.194][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.197][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.207][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[2024-11-20 05:40:13.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.248][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[2024-11-20 05:40:13.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.256][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[2024-11-20 05:40:13.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.264][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[2024-11-20 05:40:13.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.298][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.DEBUG[2024-11-20 05:40:13.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.347][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[2024-11-20 05:40:13.349][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-20 05:40:13.351][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-20 05:40:13.353][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.355][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.356][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.357][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:13.359][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.360][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.361][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.363][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-20 05:40:13.364][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-20 05:40:13.365][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:13.367][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.368][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-20 05:40:13.369][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-20 05:40:13.371][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-20 05:40:13.372][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.373][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:13.373][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:13.373][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:13.375][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-20 05:40:13.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.379][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:13.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.382][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.384][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:40:13.384][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-20 05:40:13.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:13.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:13.387][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.389][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-20 05:40:13.389][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-20 05:40:13.391][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-20 05:40:13.393][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-20 05:40:13.395][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-20 05:40:13.397][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-20 05:40:13.399][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-20 05:40:13.401][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-20 05:40:13.406][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-20 05:40:13.407][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-20 05:40:13.409][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-20 05:40:13.411][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-20 05:40:13.412][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-20 05:40:13.414][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-20 05:40:13.415][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-20 05:40:13.417][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-20 05:40:13.419][biodb::testThat]
biodb.INFO [2024-11-20 05:40:13.420][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-11-20 05:40:13.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:13.422][biodb::testThat]
biodb.DEBUG[2024-11-20 05:40:13.426][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-20 05:40:13.431][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:13.433][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-20 05:40:13.435][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:13.437][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-20 05:40:13.441][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[2024-11-20 05:40:13.445][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:13.447][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-20 05:40:13.449][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:13.451][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2024-11-20 05:40:13.461][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-20 05:40:13.463][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-20 05:40:13.464][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-20 05:40:13.466][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-20 05:40:13.467][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:13.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:13.469][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.471][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.472][FUN] Functions in observer BiodbConfig: [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 [2024-11-20 05:40:13.478][biodb::testContext]
biodb.INFO [2024-11-20 05:40:13.479][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-20 05:40:13.480][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-11-20 05:40:13.482][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-20 05:40:13.483][biodb::testContext]
biodb.INFO [2024-11-20 05:40:13.485][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-20 05:40:13.488][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-20 05:40:13.492][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:13.494][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-20 05:40:13.495][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-20 05:40:13.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.500][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-20 05:40:13.501][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-20 05:40:13.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.506][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-20 05:40:13.508][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-20 05:40:13.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.513][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-20 05:40:13.514][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-20 05:40:13.516][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-20 05:40:13.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.521][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-20 05:40:13.522][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-20 05:40:13.524][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-20 05:40:13.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.529][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-20 05:40:13.530][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-20 05:40:13.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.534][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.DEBUG[2024-11-20 05:40:13.535][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-20 05:40:13.537][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-20 05:40:13.538][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-20 05:40:13.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.543][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-20 05:40:13.545][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-20 05:40:13.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.548][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[2024-11-20 05:40:13.550][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-20 05:40:13.551][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-20 05:40:13.561][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-20 05:40:13.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.566][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-20 05:40:13.567][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-20 05:40:13.569][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-20 05:40:13.570][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-20 05:40:13.571][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-20 05:40:13.573][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-20 05:40:13.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.578][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-20 05:40:13.579][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-20 05:40:13.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.585][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-20 05:40:13.586][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-20 05:40:13.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.591][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-20 05:40:13.593][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-20 05:40:13.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.598][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-20 05:40:13.599][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-20 05:40:13.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.604][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-20 05:40:13.606][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-20 05:40:13.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.611][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-20 05:40:13.612][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-20 05:40:13.618][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-20 05:40:13.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.623][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-20 05:40:13.625][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-20 05:40:13.626][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-20 05:40:13.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.632][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-20 05:40:13.634][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.636][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-20 05:40:13.637][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:13.640][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.645][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.646][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-20 05:40:13.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:13.649][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.651][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-20 05:40:13.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:13.653][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.655][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.656][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:13.656][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:13.656][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:13.656][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-20 05:40:13.656][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-20 05:40:13.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:13.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:13.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.665][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.666][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.668][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:13.670][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:13.672][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.673][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.675][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-20 05:40:13.678][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.679][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-20 05:40:13.681][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.682][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:13.684][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.685][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.687][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.688][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.690][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-20 05:40:13.691][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:13.692][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.694][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-20 05:40:13.695][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:13.697][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.698][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.700][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:13.700][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:13.700][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:13.700][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-20 05:40:13.700][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-20 05:40:13.702][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:13.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.706][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:13.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.710][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.712][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:13.715][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:13.716][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.718][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.719][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-20 05:40:13.722][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.724][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-20 05:40:13.725][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.727][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:13.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.730][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.731][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.733][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.734][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-20 05:40:13.736][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:13.737][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.739][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-20 05:40:13.740][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:13.742][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.743][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.745][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.746][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:13.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.750][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:13.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.754][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.756][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.757][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:13.758][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:13.760][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.761][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.763][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-20 05:40:13.765][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.767][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-20 05:40:13.768][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.770][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:13.771][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.773][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.774][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.776][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.777][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-20 05:40:13.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:13.780][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.781][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-20 05:40:13.783][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:13.784][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.786][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:13.787][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.788][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-20 05:40:13.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.792][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:13.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:13.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:13.797][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:13.798][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.799][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:13.801][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:13.802][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:13.803][self$setPropertyValue]
biodb.DEBUG[2024-11-20 05:40:13.812][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:13.813][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.852][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.DEBUG[2024-11-20 05:40:13.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.864][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[2024-11-20 05:40:13.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.902][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[2024-11-20 05:40:13.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:13.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:13.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:13.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:13.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:13.922][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-20 05:40:13.924][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-20 05:40:13.926][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-20 05:40:13.928][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-20 05:40:13.930][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-20 05:40:13.932][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-20 05:40:13.934][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-20 05:40:13.936][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-20 05:40:13.938][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-20 05:40:13.940][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-20 05:40:13.942][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-20 05:40:13.944][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-20 05:40:13.946][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-20 05:40:13.948][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-20 05:40:13.949][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-20 05:40:13.951][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-20 05:40:13.953][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-20 05:40:13.955][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-20 05:40:13.957][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-20 05:40:13.959][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-20 05:40:13.961][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-20 05:40:13.963][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-20 05:40:13.965][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-20 05:40:13.967][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-20 05:40:13.969][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-20 05:40:13.970][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-20 05:40:13.972][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-20 05:40:13.974][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-20 05:40:13.976][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-20 05:40:13.978][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-20 05:40:13.980][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-20 05:40:13.982][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-20 05:40:13.984][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-20 05:40:13.986][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-20 05:40:13.988][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-20 05:40:13.990][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-20 05:40:13.992][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-20 05:40:13.994][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-20 05:40:13.996][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-20 05:40:13.998][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-20 05:40:14.000][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-20 05:40:14.002][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-20 05:40:14.004][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-20 05:40:14.006][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-20 05:40:14.008][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-20 05:40:14.009][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-20 05:40:14.011][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-20 05:40:14.013][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-20 05:40:14.015][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-20 05:40:14.017][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-20 05:40:14.019][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-20 05:40:14.021][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-20 05:40:14.023][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-20 05:40:14.025][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-20 05:40:14.027][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-20 05:40:14.029][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-20 05:40:14.031][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-20 05:40:14.033][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-20 05:40:14.035][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-20 05:40:14.044][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-20 05:40:14.046][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-20 05:40:14.048][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-20 05:40:14.050][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-20 05:40:14.052][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-20 05:40:14.054][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-20 05:40:14.056][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-20 05:40:14.059][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-20 05:40:14.061][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-20 05:40:14.063][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-20 05:40:14.065][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-20 05:40:14.067][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-20 05:40:14.069][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-20 05:40:14.071][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-20 05:40:14.073][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-20 05:40:14.075][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-20 05:40:14.077][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-20 05:40:14.079][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-20 05:40:14.081][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-20 05:40:14.083][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-20 05:40:14.085][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-20 05:40:14.087][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-20 05:40:14.090][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-20 05:40:14.092][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-20 05:40:14.094][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-20 05:40:14.096][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-20 05:40:14.098][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-20 05:40:14.099][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.102][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.202][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[2024-11-20 05:40:14.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-20 05:40:14.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-20 05:40:14.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.255][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[2024-11-20 05:40:14.257][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.1/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-20 05:40:14.259][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-20 05:40:14.261][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:14.263][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-20 05:40:14.264][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:14.266][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-20 05:40:14.267][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:14.268][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-20 05:40:14.270][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:14.271][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-20 05:40:14.273][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-20 05:40:14.274][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-20 05:40:14.275][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:14.284][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-20 05:40:14.285][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-20 05:40:14.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-20 05:40:14.288][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-20 05:40:14.290][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-20 05:40:14.290][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-20 05:40:14.290][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-20 05:40:14.291][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-20 05:40:14.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:14.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:14.295][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-20 05:40:14.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-20 05:40:14.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-20 05:40:14.299][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-20 05:40:14.301][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-20 05:40:14.301][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-20 05:40:14.302][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-20 05:40:14.303][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-20 05:40:14.305][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-20 05:40:14.306][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-20 05:40:14.306][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-20 05:40:14.308][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-20 05:40:14.310][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-20 05:40:14.312][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-20 05:40:14.314][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-20 05:40:14.316][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-20 05:40:14.319][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-20 05:40:14.323][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-20 05:40:14.324][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-20 05:40:14.326][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-20 05:40:14.328][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-20 05:40:14.330][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-20 05:40:14.331][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-20 05:40:14.333][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-20 05:40:14.334][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-20 05:40:14.336][biodb::testThat]
biodb.INFO [2024-11-20 05:40:14.338][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-11-20 05:40:14.339][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-20 05:40:14.340][biodb::testThat]
biodb.DEBUG[2024-11-20 05:40:14.344][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-20 05:40:14.349][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:14.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-20 05:40:14.353][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:14.355][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-20 05:40:14.359][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[2024-11-20 05:40:14.363][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-20 05:40:14.365][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-20 05:40:14.367][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:14.368][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-11-20 05:40:14.374][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-11-20 05:40:14.375][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-20 05:40:14.378][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-11-20 05:40:14.379][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-20 05:40:14.384][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2024-11-20 05:40:14.385][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-20 05:40:14.387][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-20 05:40:14.388][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-20 05:40:14.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-20 05:40:14.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-20 05:40:14.409][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.411][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.414][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.421][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:14.423][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:14.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.425][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.428][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-20 05:40:14.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-20 05:40:14.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.433][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:14.435][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:14.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.437][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.440][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-20 05:40:14.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-20 05:40:14.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.445][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-20 05:40:14.447][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-20 05:40:14.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.449][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.452][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-20 05:40:14.453][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-20 05:40:14.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.456][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.458][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:14.459][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:14.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.462][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.464][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:14.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-20 05:40:14.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.469][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:14.471][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:14.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.473][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.476][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-20 05:40:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-20 05:40:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.481][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:14.483][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:14.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.485][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:14.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-20 05:40:14.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.493][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:14.495][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:14.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.497][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-20 05:40:14.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-20 05:40:14.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.506][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:14.507][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:14.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.510][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.512][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-20 05:40:14.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-20 05:40:14.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.518][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:14.519][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:14.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.522][ef$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.524][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-20 05:40:14.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-20 05:40:14.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:14.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:14.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:14.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:14.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-20 05:40:14.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-20 05:40:14.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-20 05:40:14.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-20 05:40:14.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-20 05:40:14.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-20 05:40:14.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-20 05:40:14.591][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-11-20 05:40:14.596][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-20 05:40:14.598][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-20 05:40:14.599][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-20 05:40:14.601][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-20 05:40:14.602][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-20 05:40:14.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-20 05:40:14.604][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-20 05:40:14.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-20 05:40:14.607][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-20 05:40:14.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 368 ]
>
> proc.time()
user system elapsed
22.707 23.801 139.937
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.221 | 0.065 | 5.523 | |
| ChebiEntry | 0.309 | 0.543 | 3.097 | |