Pierrick Roger
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_17 |
| git_last_commit: f213a8b |
| git_last_commit_date: 2023-04-25 11:32:59 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 195/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.6.0 (landing page) Pierrick Roger
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the biodbChebi package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.6.0.tar.gz |
| StartedAt: 2023-10-17 05:42:18 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 05:45:13 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 174.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biodbChebi.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.6.0’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 2.589 0.688 7.258
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2023-10-17 05:43:38.361][biodb::testContext]
biodb.INFO [2023-10-17 05:43:38.369][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:43:38.370][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-10-17 05:43:38.371][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:43:38.376][biodb::testContext]
biodb.INFO [2023-10-17 05:43:38.392][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:43:38.396][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-17 05:43:38.410][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:43:38.415][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-17 05:43:38.416][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-17 05:43:38.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.422][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-17 05:43:38.461][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-17 05:43:38.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.471][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-17 05:43:38.472][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-17 05:43:38.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.479][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-17 05:43:38.483][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-17 05:43:38.485][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-17 05:43:38.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.492][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-17 05:43:38.494][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-17 05:43:38.496][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-17 05:43:38.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.503][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-17 05:43:38.507][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-17 05:43:38.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.514][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-17 05:43:38.515][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-17 05:43:38.519][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-17 05:43:38.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.526][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-17 05:43:38.528][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-17 05:43:38.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.535][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[2023-10-17 05:43:38.539][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-17 05:43:38.540][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-17 05:43:38.544][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-17 05:43:38.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.552][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:43:38.553][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-17 05:43:38.556][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-17 05:43:38.557][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-17 05:43:38.559][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-17 05:43:38.563][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-17 05:43:38.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.570][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-17 05:43:38.572][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-17 05:43:38.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.581][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-17 05:43:38.582][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-17 05:43:38.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.590][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-17 05:43:38.592][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-17 05:43:38.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.602][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-17 05:43:38.603][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-17 05:43:38.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.613][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-17 05:43:38.615][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-17 05:43:38.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.621][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:43:38.625][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-17 05:43:38.665][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-17 05:43:38.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.674][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-17 05:43:38.680][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-17 05:43:38.681][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-17 05:43:38.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:38.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:38.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:38.691][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-17 05:43:38.776][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.802][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-17 05:43:38.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:43:38.808][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.812][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.814][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.818][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:43:38.819][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:43:38.820][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.825][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-17 05:43:38.826][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:43:38.827][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.832][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.834][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:43:38.834][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:43:38.834][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:43:38.834][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:43:38.834][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:43:38.835][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:43:38.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:38.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:38.842][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:43:38.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:38.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:38.847][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.848][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.853][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:43:38.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:43:38.856][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.858][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.859][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-17 05:43:38.865][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.866][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:43:38.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.870][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:43:38.871][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.877][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.878][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.880][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:43:38.882][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:43:38.883][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.884][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-17 05:43:38.889][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:43:38.890][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.892][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.894][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:43:38.894][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:43:38.894][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:43:38.894][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:43:38.894][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:43:38.896][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:43:38.897][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:38.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:38.903][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:43:38.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:38.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:38.908][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.909][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.910][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:43:38.914][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:43:38.915][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.917][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.920][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-17 05:43:38.922][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.926][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-17 05:43:38.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.928][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:43:38.932][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.938][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.939][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:43:38.940][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:43:38.944][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.945][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-17 05:43:38.946][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:43:38.950][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.952][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.953][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.955][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:43:38.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:38.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:38.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:43:38.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:38.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:38.965][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.969][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.971][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:43:38.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:43:38.975][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.977][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:38.980][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-17 05:43:38.983][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.984][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:43:38.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:43:38.988][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:38.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.993][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:38.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:43:38.998][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:43:38.999][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:43:39.000][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:39.005][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-17 05:43:39.007][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:43:39.008][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:39.011][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:39.012][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:39.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:43:39.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:39.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:39.019][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:43:39.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:39.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:39.024][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:43:39.025][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:39.028][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:43:39.029][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:43:39.030][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:39.034][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:43:39.041][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:43:39.043][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.096][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[2023-10-17 05:43:39.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.130][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[2023-10-17 05:43:39.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.158][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.DEBUG[2023-10-17 05:43:39.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.207][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[2023-10-17 05:43:39.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.228][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[2023-10-17 05:43:39.229][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-17 05:43:39.236][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-17 05:43:39.242][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-17 05:43:39.243][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-17 05:43:39.249][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:43:39.251][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-17 05:43:39.254][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-17 05:43:39.256][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-17 05:43:39.261][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-17 05:43:39.263][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-17 05:43:39.267][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:43:39.269][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-17 05:43:39.273][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-17 05:43:39.275][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-17 05:43:39.291][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-17 05:43:39.293][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:43:39.297][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-17 05:43:39.298][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-17 05:43:39.303][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:43:39.305][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-17 05:43:39.306][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-17 05:43:39.311][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-17 05:43:39.315][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-17 05:43:39.317][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-17 05:43:39.322][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-17 05:43:39.324][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-17 05:43:39.327][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-17 05:43:39.329][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-17 05:43:39.331][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-17 05:43:39.335][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-17 05:43:39.337][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-17 05:43:39.340][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-17 05:43:39.342][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-17 05:43:39.348][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-17 05:43:39.350][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-17 05:43:39.353][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-17 05:43:39.354][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-17 05:43:39.360][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-17 05:43:39.362][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-17 05:43:39.365][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-17 05:43:39.367][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-17 05:43:39.372][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-17 05:43:39.374][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-17 05:43:39.377][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-17 05:43:39.378][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-17 05:43:39.380][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-17 05:43:39.384][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-17 05:43:39.388][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-17 05:43:39.390][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-17 05:43:39.392][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-17 05:43:39.395][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-17 05:43:39.397][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-17 05:43:39.402][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-17 05:43:39.404][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-17 05:43:39.406][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-17 05:43:39.408][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-17 05:43:39.414][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-17 05:43:39.416][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-17 05:43:39.417][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-17 05:43:39.422][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-17 05:43:39.423][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-17 05:43:39.427][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-17 05:43:39.429][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-17 05:43:39.430][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-17 05:43:39.434][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-17 05:43:39.436][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-17 05:43:39.440][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:43:39.442][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:43:39.447][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-17 05:43:39.449][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-17 05:43:39.451][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-17 05:43:39.453][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-17 05:43:39.455][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-17 05:43:39.461][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-17 05:43:39.462][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-17 05:43:39.465][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-17 05:43:39.467][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-17 05:43:39.473][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-17 05:43:39.475][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-17 05:43:39.478][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-17 05:43:39.480][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-17 05:43:39.485][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-17 05:43:39.487][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-17 05:43:39.498][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-17 05:43:39.500][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:43:39.509][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:43:39.511][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.513][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.535][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[2023-10-17 05:43:39.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.547][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[2023-10-17 05:43:39.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.653][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[2023-10-17 05:43:39.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.668][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[2023-10-17 05:43:39.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.700][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[2023-10-17 05:43:39.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.713][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[2023-10-17 05:43:39.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:39.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:43:39.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:39.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:39.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:39.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:39.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:39.740][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[2023-10-17 05:43:39.743][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-10-17 05:43:39.761][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-10-17 05:43:39.777][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:39.778][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-17 05:43:39.780][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:39.785][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:43:39.786][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:39.787][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:43:39.790][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:39.791][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-10-17 05:43:39.795][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-10-17 05:43:39.797][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:43:39.798][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:39.801][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-10-17 05:43:39.802][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-10-17 05:43:39.804][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-10-17 05:43:39.808][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-17 05:43:39.810][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:43:39.810][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:43:39.810][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:43:39.811][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-17 05:43:39.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:39.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:39.816][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:43:39.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:43:39.822][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:43:39.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:43:39.824][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:39.824][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-10-17 05:43:39.828][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:43:39.830][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:43:39.831][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-17 05:43:39.834][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-10-17 05:43:39.834][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-10-17 05:43:39.846][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:43:39.848][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:43:39.854][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-10-17 05:43:39.856][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:43:39.860][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:43:39.865][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:43:39.921][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-10-17 05:43:39.923][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-10-17 05:43:39.934][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-10-17 05:43:39.940][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-10-17 05:43:39.947][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-17 05:43:39.952][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-17 05:43:39.954][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-10-17 05:43:39.955][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-10-17 05:43:39.972][biodb::testThat]
biodb.INFO [2023-10-17 05:43:39.977][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-10-17 05:43:39.978][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:39.979][biodb::testThat]
biodb.TRACE[2023-10-17 05:43:39.986][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-10-17 05:43:39.989][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:39.998][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:40.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:40.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:40.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:40.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:40.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:40.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:40.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:40.070][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.072][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.077][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.078][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.109][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:40.111][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:40.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.113][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.158][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:40.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:40.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.168][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:40.170][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:40.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.173][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:40.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:40.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.181][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:40.182][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:40.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.185][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:40.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:40.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.194][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:40.196][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:40.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.199][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:40.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:40.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.208][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:40.213][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:40.215][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.216][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.218][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:40.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:40.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.227][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:40.228][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:40.232][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.234][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.235][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:40.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:40.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.245][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:40.246][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:40.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.251][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:40.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:40.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.264][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:40.265][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:40.266][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.267][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:40.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:40.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.279][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:40.283][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:40.284][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.307][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.309][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:40.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:40.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.320][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:40.321][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:40.324][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.326][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.328][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:40.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:40.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:40.477][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-10-17 05:43:40.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:40.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:40.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:40.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:40.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:40.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:40.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:40.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:40.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:40.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:40.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:40.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:40.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.572][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:43:40.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:43:40.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:43:40.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:43:40.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.588][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-17 05:43:40.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-17 05:43:40.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.598][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-17 05:43:40.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-17 05:43:40.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.823][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.828][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.829][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.830][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:40.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:40.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.880][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.884][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.886][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.889][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:40.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:40.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:40.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:40.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:40.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.934][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:40.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:40.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.941][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:40.942][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:40.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.949][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:40.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:40.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.968][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:40.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:40.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.979][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:40.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:40.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:40.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:40.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:40.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:40.998][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:40.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:41.000][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.003][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.004][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:41.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.055][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.058][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.061][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.108][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.112][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.114][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.181][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:41.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:41.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.192][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:41.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:41.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.202][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:41.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:41.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.211][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:41.212][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:41.216][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.218][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.222][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:41.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:41.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.252][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.273][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.274][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.276][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.278][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.280][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.305][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.311][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.320][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.326][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.331][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.333][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.334][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.336][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:41.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:41.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.369][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:41.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:41.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.384][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:41.386][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:41.387][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.388][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.389][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:41.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:41.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.436][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.438][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.439][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.441][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:41.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:41.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:41.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:41.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:41.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:41.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.489][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:41.491][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:41.492][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.498][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:41.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:41.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.524][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:41.525][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:41.527][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.529][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.539][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:41.540][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:41.542][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.547][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.554][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:41.559][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:41.561][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.562][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.573][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:41.575][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:41.577][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.578][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.590][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.594][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.596][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.597][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.608][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.609][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.623][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.625][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.636][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.637][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.643][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.644][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.650][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.655][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:41.656][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.657][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.667][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.673][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:41.674][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.675][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.685][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:41.689][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:41.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.691][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.703][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:41.704][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:41.708][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.709][ef$get] fields variable is a list.
biodb.INFO [2023-10-17 05:43:41.728][biodb::testThat]
biodb.INFO [2023-10-17 05:43:41.729][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-17 05:43:41.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:41.734][biodb::testThat]
biodb.DEBUG[2023-10-17 05:43:41.758][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-10-17 05:43:41.776][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:41.782][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-10-17 05:43:41.783][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:41.788][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-10-17 05:43:41.790][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:41.833][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:41.834][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:41.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:41.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:41.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:41.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:41.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:41.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:41.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:41.864][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:41.866][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:41.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.869][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:41.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:41.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.908][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:41.913][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:41.915][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.916][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.919][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:41.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:41.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.926][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:41.928][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:41.930][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.932][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.933][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:41.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:41.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.943][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:41.945][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:41.946][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.949][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:41.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:41.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.957][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.958][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.963][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.964][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:41.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.976][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.977][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.981][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.983][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.986][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:41.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:41.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:41.995][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:41.996][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:41.999][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.000][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.014][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:42.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.024][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:42.026][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:42.031][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.032][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:42.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:42.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.044][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.046][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.049][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.051][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.063][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:42.064][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:42.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.070][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.075][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:42.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:42.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.082][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:42.083][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:42.089][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.090][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.093][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:42.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:42.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:42.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:42.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:42.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:42.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:42.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:42.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:42.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:42.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:42.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:42.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:42.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:42.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:42.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:42.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:42.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:42.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:42.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:42.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:42.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:42.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:42.206][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-10-17 05:43:42.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-17 05:43:42.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-17 05:43:42.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-17 05:43:42.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-17 05:43:42.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-17 05:43:42.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-17 05:43:42.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:43:42.247][biodb::testThat]
biodb.INFO [2023-10-17 05:43:42.248][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-17 05:43:42.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:42.254][biodb::testThat]
biodb.TRACE[2023-10-17 05:43:42.260][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.262][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.265][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.267][ef$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:42.271][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-10-17 05:43:42.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:42.350][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-10-17 05:43:42.357][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-10-17 05:43:42.387][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:42.423][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-10-17 05:43:42.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:42.428][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-10-17 05:43:42.463][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[2023-10-17 05:43:42.470][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:42.472][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-10-17 05:43:42.476][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:42.478][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-10-17 05:43:42.482][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-10-17 05:43:42.506][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:42.507][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:42.509][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.511][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.512][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.513][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.514][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.518][ef$get] fields variable is a list.
biodb.INFO [2023-10-17 05:43:42.524][biodb::testThat]
biodb.INFO [2023-10-17 05:43:42.527][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-10-17 05:43:42.528][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:42.531][biodb::testThat]
biodb.TRACE[2023-10-17 05:43:42.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:42.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:42.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:42.678][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[2023-10-17 05:43:42.683][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:42.684][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-10-17 05:43:42.687][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:42.689][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-10-17 05:43:42.737][biodb::testThat]
biodb.INFO [2023-10-17 05:43:42.739][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-10-17 05:43:42.743][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:42.744][biodb::testThat]
biodb.TRACE[2023-10-17 05:43:42.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:42.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:42.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:42.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:42.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:42.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:42.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:42.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:42.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.820][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:43:42.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:43:42.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.827][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:43:42.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:43:42.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.834][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-17 05:43:42.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-17 05:43:42.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-17 05:43:42.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-17 05:43:42.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:42.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:42.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:42.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:42.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:42.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:42.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:42.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:42.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:42.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.920][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:43:42.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:43:42.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.925][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-17 05:43:42.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-17 05:43:42.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.931][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-17 05:43:42.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-17 05:43:42.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:42.939][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-17 05:43:42.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-17 05:43:42.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:42.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:43:42.953][biodb::testThat]
biodb.INFO [2023-10-17 05:43:42.955][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-17 05:43:42.956][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:42.957][biodb::testThat]
biodb.INFO [2023-10-17 05:43:42.970][biodb::testThat]
biodb.INFO [2023-10-17 05:43:42.972][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-17 05:43:42.975][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:42.977][biodb::testThat]
biodb.INFO [2023-10-17 05:43:42.991][biodb::testThat]
biodb.INFO [2023-10-17 05:43:42.994][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-17 05:43:42.996][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:42.997][biodb::testThat]
biodb.DEBUG[2023-10-17 05:43:43.005][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-10-17 05:43:43.936][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-10-17 05:43:45.066][biodb::testThat]
biodb.INFO [2023-10-17 05:43:45.067][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-17 05:43:45.071][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:45.072][biodb::testThat]
biodb.DEBUG[2023-10-17 05:43:45.644][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[2023-10-17 05:43:46.353][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:46.355][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:46.357][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.358][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:46.362][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:46.364][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:46.367][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.369][ef$get] fields variable is a list.
biodb.INFO [2023-10-17 05:43:46.372][biodb::testThat]
biodb.INFO [2023-10-17 05:43:46.375][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-10-17 05:43:46.377][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:43:46.380][biodb::testThat]
biodb.TRACE[2023-10-17 05:43:46.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:46.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:46.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:46.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:46.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:46.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:46.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:46.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:46.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:46.580][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[2023-10-17 05:43:46.585][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:46.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-10-17 05:43:46.590][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:46.594][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-10-17 05:43:46.684][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[2023-10-17 05:43:46.689][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:46.691][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-10-17 05:43:46.694][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:46.697][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-10-17 05:43:46.719][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-17 05:43:46.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-17 05:43:46.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:46.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:46.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:46.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:46.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:46.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:46.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:46.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:46.792][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[2023-10-17 05:43:46.797][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:46.799][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-10-17 05:43:46.803][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:46.805][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-10-17 05:43:46.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:46.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:46.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:46.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:46.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:46.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:46.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:46.831][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-10-17 05:43:46.897][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:46.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-10-17 05:43:46.901][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:43:46.903][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:43:46.904][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:46.907][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:46.908][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:43:46.909][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:43:46.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:46.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:46.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:46.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:46.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:46.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:46.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:46.931][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-10-17 05:43:46.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:43:46.937][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:43:46.938][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-10-17 05:43:47.487][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-10-17 05:43:48.169][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:43:48.173][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-10-17 05:43:48.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-10-17 05:43:48.201][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-10-17 05:43:48.205][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:43:48.207][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:48.210][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:48.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:48.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:48.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:48.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:48.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:48.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:48.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:48.234][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.253][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.254][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.258][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.270][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:48.272][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:48.273][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.274][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.276][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:48.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:48.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.286][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:48.287][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:48.288][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.290][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:48.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:48.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.300][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:48.303][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:48.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.307][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:48.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:48.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.316][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:48.317][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:48.319][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.320][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:48.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:48.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.328][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:48.329][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:48.330][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.331][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.333][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:48.334][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.335][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.337][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.338][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:48.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.346][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:48.348][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:48.349][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.350][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:48.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:48.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.360][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:48.361][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:48.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.364][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:48.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:48.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.374][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:48.375][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:48.377][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.379][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.382][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:48.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:48.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.389][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:48.390][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:48.391][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.392][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.395][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:48.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:48.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:48.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:48.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:48.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:48.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:48.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:48.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:48.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:48.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:48.473][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-10-17 05:43:48.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:48.512][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[2023-10-17 05:43:48.518][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:48.521][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-10-17 05:43:48.523][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:48.525][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-10-17 05:43:48.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:48.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:48.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:48.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:48.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:48.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:48.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:48.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:48.597][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:43:48.603][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:48.605][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-10-17 05:43:48.606][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:48.610][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-10-17 05:43:48.646][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[2023-10-17 05:43:48.650][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:43:48.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-10-17 05:43:48.654][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:43:48.658][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-10-17 05:43:48.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:48.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:48.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:48.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:48.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:48.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:48.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:48.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:48.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:48.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:48.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:48.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:48.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:48.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:48.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:48.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:48.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:48.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:48.719][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-10-17 05:43:48.720][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:48.723][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-10-17 05:43:48.725][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:43:48.726][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:43:48.729][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:48.730][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:48.731][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:43:48.733][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:43:48.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:48.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:48.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:48.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:48.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:48.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:48.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:48.771][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-10-17 05:43:48.804][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:43:48.807][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:43:48.828][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-10-17 05:43:49.617][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-10-17 05:43:50.312][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:43:50.316][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-10-17 05:43:50.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-10-17 05:43:50.326][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-10-17 05:43:50.330][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:43:50.332][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:50.333][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:50.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:50.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:50.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:50.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:50.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:50.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:50.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:50.356][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.359][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.360][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.361][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.370][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:50.374][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:50.375][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.376][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.379][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:50.381][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:50.382][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.384][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.386][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:50.387][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:50.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.390][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.394][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:50.395][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:50.396][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.398][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.400][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:50.402][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:50.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.406][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.408][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:50.409][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.410][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.414][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.416][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:50.417][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:50.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.422][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.425][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:50.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:50.429][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.430][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:50.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:50.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.440][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:50.442][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:50.445][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.446][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:50.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:50.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.456][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:50.457][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:50.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.462][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:50.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:50.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:50.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:50.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:50.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:50.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:50.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:50.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:50.547][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-10-17 05:43:50.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:50.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:50.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:50.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:50.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:50.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:50.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:50.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:50.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:50.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:50.605][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[2023-10-17 05:43:50.607][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-10-17 05:43:50.612][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:50.614][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-10-17 05:43:50.616][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:43:50.618][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:43:50.619][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:50.621][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:50.622][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:43:50.624][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:43:50.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:50.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:50.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:50.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:50.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:50.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:50.647][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[2023-10-17 05:43:50.649][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-10-17 05:43:50.653][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:43:50.654][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:43:50.655][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-10-17 05:43:51.402][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-10-17 05:43:52.046][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:43:52.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-10-17 05:43:52.054][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-10-17 05:43:52.061][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-10-17 05:43:52.065][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:43:52.067][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:52.069][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:52.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:52.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:52.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:52.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:52.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:52.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:52.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:52.094][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.095][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.098][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.107][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:52.108][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:52.109][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.113][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.115][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:52.118][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:52.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.120][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.122][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:52.124][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:52.127][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.128][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.130][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:52.134][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:52.136][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.137][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.139][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:52.140][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:52.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.143][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.145][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:52.148][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.150][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:52.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:52.157][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.159][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.161][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:52.165][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:52.166][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.168][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:52.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:52.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.180][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:52.182][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:52.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.185][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.187][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:52.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:52.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.192][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:52.194][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:52.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.197][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:52.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:52.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:52.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:52.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:52.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:52.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:52.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:52.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:52.269][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-10-17 05:43:52.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:52.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:52.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:52.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:52.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:52.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:52.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:52.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:52.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:52.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:52.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:52.311][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-10-17 05:43:52.312][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:52.314][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-10-17 05:43:52.316][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:43:52.317][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:43:52.319][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:52.320][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:52.322][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:43:52.323][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:43:52.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:52.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:52.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:52.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:52.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:52.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:52.341][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[2023-10-17 05:43:52.343][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-10-17 05:43:52.347][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:43:52.348][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:43:52.350][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-10-17 05:43:53.026][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-10-17 05:43:53.721][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:43:53.727][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-10-17 05:43:53.733][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-10-17 05:43:53.738][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-10-17 05:43:53.742][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:43:53.744][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:53.746][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:53.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:53.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:53.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:53.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:53.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:53.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:53.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:53.771][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.772][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.773][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.776][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.787][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:53.789][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:53.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.794][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.796][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:53.798][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:53.799][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.801][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.802][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:53.804][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:53.805][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.806][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.809][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:53.811][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:53.816][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.818][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.820][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:53.822][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:53.823][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.825][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.826][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:53.828][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.829][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.830][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.832][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:53.834][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:53.836][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.837][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.854][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:53.856][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:53.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.858][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:53.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:53.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.868][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:53.872][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:53.874][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.875][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.877][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:53.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:53.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.884][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:53.885][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:53.888][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.890][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:53.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:53.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:53.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:53.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:53.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:53.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:53.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:53.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:53.960][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-10-17 05:43:53.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:53.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:53.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:53.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:53.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:53.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:53.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:54.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:54.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:54.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:54.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:54.013][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-10-17 05:43:54.015][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:54.017][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-10-17 05:43:54.019][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:43:54.021][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:43:54.022][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:54.024][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:54.025][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:43:54.027][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:43:54.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:54.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:54.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:54.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:54.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:54.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:54.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:54.049][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-10-17 05:43:54.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:43:54.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:43:54.056][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-10-17 05:43:54.768][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-10-17 05:43:55.532][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:43:55.534][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-10-17 05:43:55.540][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-10-17 05:43:55.543][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-10-17 05:43:55.546][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:43:55.548][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:55.550][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:55.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:55.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:55.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:55.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:55.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:55.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:55.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:55.574][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.576][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.577][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.578][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.596][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:55.597][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:55.598][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.600][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.602][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:55.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:55.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.608][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:55.609][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:55.611][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.612][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:55.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:55.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.619][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:55.620][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:55.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.623][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.624][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:55.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:55.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.629][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:55.631][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:55.633][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.634][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:55.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:55.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.643][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:55.645][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:55.647][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.648][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.649][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:55.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:55.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.655][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:55.656][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:55.657][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.658][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.660][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:55.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:55.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.665][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:55.666][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:55.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.672][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:55.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:55.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.681][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:55.683][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:55.685][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.686][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:55.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:55.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.694][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:55.695][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:55.697][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.698][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.699][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:55.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:55.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.704][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:55.706][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:55.707][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.708][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.710][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:55.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:55.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:55.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:55.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:55.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:55.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:55.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:55.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:55.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:55.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:55.775][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-10-17 05:43:55.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:55.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:55.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:55.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:55.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:55.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:55.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:55.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:55.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:55.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:55.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:55.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:55.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:55.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:55.804][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-10-17 05:43:55.805][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:55.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-10-17 05:43:55.809][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:43:55.811][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:43:55.813][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:55.814][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:55.815][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:43:55.816][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:43:55.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:55.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:55.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:55.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:55.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:55.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:55.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:55.845][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-10-17 05:43:55.849][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:43:55.850][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:43:55.853][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-10-17 05:43:56.451][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-10-17 05:43:57.254][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:43:57.259][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-10-17 05:43:57.266][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-10-17 05:43:57.273][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-10-17 05:43:57.275][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:43:57.279][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:57.280][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:57.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:57.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:57.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:57.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:57.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:57.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:57.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:57.305][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.308][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.309][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.310][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.321][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:57.322][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:57.326][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.328][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.329][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:57.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:57.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.340][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:57.342][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:57.343][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.347][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.349][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:57.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:57.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.360][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:57.361][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:57.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.366][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:57.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:57.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.375][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:57.379][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:57.380][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.382][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:57.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:57.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.394][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:57.395][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:57.399][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.400][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.401][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:57.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:57.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.410][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:57.412][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:57.413][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.416][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.418][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:57.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:57.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.427][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:57.429][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:57.430][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.432][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:57.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:57.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.443][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:57.445][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:57.446][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.447][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:57.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:57.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.458][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:57.460][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:57.461][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.465][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.467][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:57.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:57.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.472][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:57.478][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:57.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.481][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.486][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:57.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:57.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:57.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:57.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:57.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:57.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:57.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:57.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:57.594][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-10-17 05:43:57.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:57.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:57.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:57.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:57.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:57.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:57.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:57.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:57.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:57.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:57.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:57.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:57.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:57.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:57.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:57.639][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-10-17 05:43:57.643][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:57.645][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-10-17 05:43:57.650][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:43:57.653][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:43:57.655][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:57.656][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:57.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:43:57.661][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:43:57.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:57.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:57.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:57.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:57.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:57.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:57.683][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[2023-10-17 05:43:57.685][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-10-17 05:43:57.689][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:43:57.691][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:43:57.693][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-10-17 05:43:58.591][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-10-17 05:43:59.170][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-10-17 05:43:59.174][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-10-17 05:43:59.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-10-17 05:43:59.186][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-10-17 05:43:59.191][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-10-17 05:43:59.197][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:43:59.199][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:43:59.200][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:43:59.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:59.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:59.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:59.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:59.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:59.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:59.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:43:59.230][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.236][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.238][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.239][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.252][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:59.256][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:59.257][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.258][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.259][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:43:59.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:43:59.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.269][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:59.271][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:59.272][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.277][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.278][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:43:59.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:43:59.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.284][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:59.289][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:59.290][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.293][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:43:59.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:43:59.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.304][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:59.306][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:59.307][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.308][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:43:59.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:43:59.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.321][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:59.322][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:43:59.327][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.329][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.331][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:59.332][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:59.333][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.334][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.341][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:43:59.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:59.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.347][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:59.353][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:59.355][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.378][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:59.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:43:59.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.390][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:59.391][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:59.392][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.395][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:43:59.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:43:59.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.408][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:59.410][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:59.412][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.413][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:43:59.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:43:59.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.424][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:59.425][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:59.426][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.431][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.433][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:43:59.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:43:59.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:59.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:59.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:59.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:59.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:43:59.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:43:59.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:43:59.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:43:59.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:59.506][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-10-17 05:43:59.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:59.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:59.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:59.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:59.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:43:59.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:59.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:43:59.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:43:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:43:59.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:59.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:59.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:59.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:59.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:59.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:59.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:59.550][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-10-17 05:43:59.551][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:43:59.554][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-10-17 05:43:59.556][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:43:59.558][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:43:59.561][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:43:59.565][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:43:59.567][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:43:59.568][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:43:59.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:43:59.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:43:59.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:43:59.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:43:59.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:43:59.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:43:59.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:43:59.592][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-10-17 05:43:59.597][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:43:59.598][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:43:59.600][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-10-17 05:44:00.148][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-10-17 05:44:00.769][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:00.776][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-10-17 05:44:00.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-10-17 05:44:00.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-10-17 05:44:00.788][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:00.790][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:00.791][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:00.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:00.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:00.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:00.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:00.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:00.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:00.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:00.816][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:00.818][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:00.820][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.822][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:00.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:00.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.850][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:00.851][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:00.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.853][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:00.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:00.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.864][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:00.866][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:00.867][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.868][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:00.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:00.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.879][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:00.882][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:00.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.884][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:00.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:00.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.892][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:00.894][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:00.897][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.898][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:00.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:00.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.908][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:00.909][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:00.911][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.912][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.914][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:00.915][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:00.916][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.918][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.921][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:00.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:00.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.929][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:00.932][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:00.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.934][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:00.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:00.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.944][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:00.945][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:00.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.950][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:00.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:00.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.959][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:00.960][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:00.961][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.965][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.967][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:00.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:00.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.974][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:00.975][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:00.976][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.977][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.979][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:00.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:00.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:00.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:00.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:00.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:00.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:00.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:01.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:01.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:01.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:01.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:01.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:01.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:01.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:01.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:01.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:01.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:01.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:01.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:01.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:01.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:01.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:01.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:01.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:01.059][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-10-17 05:44:01.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:01.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:01.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:01.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:01.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:01.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:01.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:01.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:01.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:01.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:01.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:01.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:01.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:01.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:01.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:01.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:01.097][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-10-17 05:44:01.098][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:01.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-10-17 05:44:01.104][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:01.106][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:01.107][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:01.108][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:01.111][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:01.113][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:01.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:01.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:01.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:01.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:01.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:01.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:01.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:01.149][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-10-17 05:44:01.153][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:01.155][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:01.157][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-10-17 05:44:01.757][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-10-17 05:44:02.371][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2023-10-17 05:44:02.374][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-10-17 05:44:02.376][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-10-17 05:44:02.381][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-10-17 05:44:02.388][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-10-17 05:44:02.391][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:02.393][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:02.395][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:02.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:02.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:02.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:02.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:02.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:02.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:02.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:02.420][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.422][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.423][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.426][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.436][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:02.437][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:02.439][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.440][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.442][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:02.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:02.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.449][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:02.451][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:02.453][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.454][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:02.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.464][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:02.467][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:02.468][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.469][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:02.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:02.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.479][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:02.482][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:02.483][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.484][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:02.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:02.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.494][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:02.496][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:02.497][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.498][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.500][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:02.502][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:02.503][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.504][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.507][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:02.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:02.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:02.514][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:02.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.516][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:02.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:02.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.526][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:02.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:02.530][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.531][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:02.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:02.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.538][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:02.539][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:02.543][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.544][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.546][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:02.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:02.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.553][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:02.554][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:02.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.557][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.559][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:02.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:02.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:02.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:02.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:02.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:02.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:02.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:02.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:02.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:02.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:02.656][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-10-17 05:44:02.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:02.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:02.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:02.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:02.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:02.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:02.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:02.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:02.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:02.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:02.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:02.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:02.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:02.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:02.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:02.700][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[2023-10-17 05:44:02.701][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-10-17 05:44:02.703][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:02.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-10-17 05:44:02.707][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:02.708][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:02.710][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:02.715][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:02.716][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:02.717][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:02.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:02.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:02.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:02.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:02.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:02.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:02.740][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[2023-10-17 05:44:02.741][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-10-17 05:44:02.746][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:02.748][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:02.750][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-10-17 05:44:03.439][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-10-17 05:44:04.016][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:04.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-10-17 05:44:04.023][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-10-17 05:44:04.030][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-10-17 05:44:04.032][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:04.036][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:04.037][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:04.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:04.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:04.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:04.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:04.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:04.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:04.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:04.058][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.060][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.062][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.069][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:04.071][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:04.072][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.073][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.075][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:04.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:04.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.084][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:04.085][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:04.086][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.087][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:04.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:04.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.095][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:04.096][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:04.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.102][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:04.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:04.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.109][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:04.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:04.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.112][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:04.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:04.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.120][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:04.122][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:04.123][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.124][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.129][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:04.130][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:04.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.132][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.134][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:04.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:04.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.139][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:04.140][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:04.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.144][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:04.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:04.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.207][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:04.211][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:04.213][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.216][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.218][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:04.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:04.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.228][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:04.229][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:04.230][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.232][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.235][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:04.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:04.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.245][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:04.247][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:04.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.251][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.252][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:04.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:04.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:04.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:04.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:04.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:04.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:04.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:04.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:04.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:04.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:04.341][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-10-17 05:44:04.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:04.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:04.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:04.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:04.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:04.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:04.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:04.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:04.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:04.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:04.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:04.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:04.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:04.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:04.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:04.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:04.385][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-10-17 05:44:04.387][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:04.390][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-10-17 05:44:04.393][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:04.395][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:04.396][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:04.399][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:04.400][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:04.404][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:04.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:04.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:04.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:04.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:04.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:04.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:04.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:04.427][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-10-17 05:44:04.432][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:04.433][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:04.438][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-10-17 05:44:05.115][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-10-17 05:44:05.778][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:05.784][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-10-17 05:44:05.790][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-10-17 05:44:05.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-10-17 05:44:05.803][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:05.805][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:05.808][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:05.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:05.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:05.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:05.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:05.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:05.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:05.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:05.835][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:05.836][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:05.839][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.841][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:05.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:05.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.851][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:05.852][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:05.853][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.859][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.860][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:05.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:05.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.890][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:05.891][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:05.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.896][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:05.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:05.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.907][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:05.908][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:05.910][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.913][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:05.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:05.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.925][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:05.926][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:05.927][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.930][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:05.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:05.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.939][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:05.943][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:05.944][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.945][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.949][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:05.950][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:05.952][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.955][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.956][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:05.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:05.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.966][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:05.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:05.969][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.970][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:05.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:05.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.982][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:05.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:05.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.988][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:05.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:05.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:05.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:05.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.000][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:06.002][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:06.004][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.005][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.006][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:06.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:06.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.016][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:06.017][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:06.018][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.023][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:06.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:06.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:06.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:06.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:06.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:06.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:06.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:06.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:06.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:06.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:06.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:06.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:06.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:06.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:06.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:06.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:06.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:06.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:06.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:06.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:06.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:06.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:06.114][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-10-17 05:44:06.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:06.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:06.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:06.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:06.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:06.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:06.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:06.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:06.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:06.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:06.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:06.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:06.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:06.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:06.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:06.158][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.DEBUG[2023-10-17 05:44:06.159][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-10-17 05:44:06.162][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:06.163][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2023-10-17 05:44:06.167][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:06.169][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:06.170][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:06.174][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:06.175][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:06.176][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:06.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:06.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:06.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:06.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:06.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:06.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:06.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:06.219][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-10-17 05:44:06.224][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:06.227][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:06.228][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-10-17 05:44:06.816][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-10-17 05:44:07.438][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:07.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-10-17 05:44:07.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-10-17 05:44:07.452][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-10-17 05:44:07.455][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:07.457][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:07.459][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:07.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:07.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:07.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:07.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:07.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:07.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:07.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:07.485][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.486][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.488][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.489][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.500][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:07.501][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:07.503][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.504][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.505][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:07.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:07.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.512][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:07.514][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:07.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.517][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:07.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:07.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.525][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:07.527][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:07.528][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.532][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.535][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:07.537][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:07.539][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.540][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.543][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:07.544][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:07.545][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.548][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.550][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:07.552][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:07.554][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.555][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.558][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:07.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:07.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.563][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:07.568][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:07.569][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.570][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:07.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:07.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.578][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:07.579][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:07.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.583][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:07.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:07.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.594][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:07.595][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:07.597][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.598][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.600][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:07.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:07.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.609][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:07.611][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:07.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.614][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:07.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:07.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:07.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:07.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:07.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:07.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:07.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:07.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:07.691][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-10-17 05:44:07.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:07.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:07.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:07.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:07.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:07.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:07.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:07.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:07.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:07.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:07.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:07.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:07.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:07.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:07.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:07.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:07.768][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-10-17 05:44:07.771][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:07.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-10-17 05:44:07.779][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:07.780][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:07.783][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:07.784][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:07.786][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:07.790][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:07.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:07.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:07.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:07.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:07.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:07.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:07.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:07.816][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-10-17 05:44:07.823][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:07.824][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:07.827][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-10-17 05:44:08.471][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-10-17 05:44:09.105][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:09.109][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-10-17 05:44:09.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-10-17 05:44:09.122][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-10-17 05:44:09.124][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:09.129][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:09.130][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:09.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:09.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:09.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:09.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:09.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:09.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:09.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:09.155][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.156][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.162][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.174][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:09.175][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:09.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.179][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.181][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:09.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:09.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.188][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:09.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:09.192][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.193][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:09.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:09.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.205][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:09.206][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:09.211][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.212][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.213][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:09.217][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:09.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.219][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.223][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:09.224][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:09.225][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.230][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.231][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:09.232][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:09.235][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.236][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.242][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:09.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:09.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.248][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:09.249][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:09.250][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.255][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:09.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:09.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.262][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:09.267][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:09.268][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.269][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:09.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:09.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.280][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:09.281][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:09.282][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.287][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.288][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:09.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:09.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.293][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:09.298][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:09.299][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.301][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:09.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:09.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:09.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:09.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:09.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:09.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:09.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:09.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:09.402][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-10-17 05:44:09.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:09.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:09.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:09.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:09.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:09.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:09.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:09.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:09.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:09.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:09.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:09.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:09.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:09.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:09.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:09.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:09.450][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-10-17 05:44:09.454][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:09.456][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-10-17 05:44:09.461][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:09.463][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:09.464][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:09.467][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:09.469][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:09.473][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:09.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:09.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:09.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:09.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:09.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:09.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:09.498][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[2023-10-17 05:44:09.500][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-10-17 05:44:09.507][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:09.508][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:09.510][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-10-17 05:44:10.128][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-10-17 05:44:10.975][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:10.980][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-10-17 05:44:10.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-10-17 05:44:10.991][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-10-17 05:44:10.994][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:10.995][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:10.997][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:11.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:11.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:11.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:11.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:11.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:11.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:11.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:11.027][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.031][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.032][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.033][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.045][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:11.046][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:11.047][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.050][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.051][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:11.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:11.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.061][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:11.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:11.064][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.065][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:11.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:11.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.077][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:11.079][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:11.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.082][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:11.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:11.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:11.100][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:11.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.103][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:11.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:11.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.114][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:11.117][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:11.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.120][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.124][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:11.125][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:11.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.130][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.132][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:11.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:11.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.157][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:11.159][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:11.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.162][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:11.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:11.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.173][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:11.175][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:11.177][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.178][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:11.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:11.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.185][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:11.186][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:11.188][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.191][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.192][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:11.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:11.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.202][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:11.205][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:11.206][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.208][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:11.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:11.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:11.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:11.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:11.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:11.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:11.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:11.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:11.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:11.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:11.276][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-10-17 05:44:11.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:11.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:11.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:11.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:11.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:11.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:11.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:11.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:11.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:11.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:11.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:11.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:11.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:11.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:11.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:11.313][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[2023-10-17 05:44:11.315][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-10-17 05:44:11.316][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:11.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-10-17 05:44:11.320][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:11.321][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:11.325][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:11.327][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:11.330][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:11.331][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:11.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:11.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:11.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:11.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:11.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:11.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:11.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:11.353][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-10-17 05:44:11.357][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:11.359][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:11.361][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-10-17 05:44:12.056][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-10-17 05:44:12.781][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:12.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-10-17 05:44:12.793][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-10-17 05:44:12.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-10-17 05:44:12.804][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:12.806][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:12.807][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:12.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:12.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:12.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:12.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:12.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:12.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:12.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:12.835][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:12.856][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:12.862][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.863][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:12.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:12.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.875][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:12.876][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:12.879][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.880][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.885][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:12.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:12.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.892][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:12.894][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:12.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.899][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.900][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:12.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:12.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.910][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:12.912][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:12.913][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.916][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.918][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:12.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:12.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.925][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:12.929][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:12.930][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.934][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:12.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:12.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.943][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:12.948][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:12.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.950][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.955][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:12.957][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:12.958][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.960][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.962][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:12.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:12.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.971][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:12.973][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:12.975][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.979][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:12.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:12.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:12.992][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:12.994][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:12.996][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:12.998][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:13.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.010][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:13.011][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:13.013][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.014][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.020][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:13.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:13.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.025][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:13.027][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:13.028][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.029][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.031][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:13.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:13.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:13.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:13.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:13.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:13.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:13.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:13.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:13.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:13.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:13.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:13.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:13.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:13.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:13.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:13.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:13.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:13.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:13.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:13.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:13.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:13.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:13.105][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-10-17 05:44:13.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:13.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:13.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:13.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:13.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:13.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:13.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:13.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:13.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:13.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:13.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:13.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:13.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:13.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:13.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:13.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:13.151][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-10-17 05:44:13.153][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:13.155][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-10-17 05:44:13.160][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:13.161][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:13.163][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:13.177][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:13.179][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:13.181][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:13.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:13.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:13.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:13.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:13.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:13.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:13.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:13.210][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-10-17 05:44:13.216][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:13.217][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:13.219][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-10-17 05:44:13.879][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-10-17 05:44:14.407][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:14.411][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-10-17 05:44:14.416][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-10-17 05:44:14.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-10-17 05:44:14.426][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:14.429][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:14.430][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:14.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:14.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:14.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:14.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:14.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:14.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:14.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:14.453][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.454][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.456][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.457][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.464][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:14.465][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:14.466][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.467][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.469][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:14.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:14.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.475][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:14.476][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:14.478][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.479][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:14.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:14.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.487][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:14.488][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:14.490][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.492][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:14.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:14.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.503][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:14.505][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:14.506][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.508][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:14.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:14.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.519][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:14.520][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:14.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.523][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.525][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:14.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:14.529][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.530][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.538][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:14.539][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:14.541][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.543][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:14.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:14.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.555][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:14.556][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:14.559][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.560][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:14.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:14.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.570][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:14.571][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:14.573][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.574][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.576][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:14.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:14.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.584][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:14.585][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:14.588][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.589][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.591][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:14.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:14.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:14.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:14.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:14.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:14.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:14.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:14.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:14.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:14.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:14.687][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-10-17 05:44:14.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:14.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:14.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:14.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:14.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:14.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:14.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:14.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:14.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:14.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:14.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:14.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:14.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:14.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:14.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:14.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:14.731][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-10-17 05:44:14.732][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:14.734][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-10-17 05:44:14.736][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:14.740][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:14.743][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:14.745][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:14.747][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:14.748][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:14.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:14.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:14.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:14.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:14.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:14.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:14.769][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[2023-10-17 05:44:14.770][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-10-17 05:44:14.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:14.776][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:14.781][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-10-17 05:44:15.366][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-10-17 05:44:16.025][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:16.027][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-10-17 05:44:16.034][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-10-17 05:44:16.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-10-17 05:44:16.043][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:16.045][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:16.046][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:16.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:16.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:16.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:16.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:16.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:16.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:16.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:16.065][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.067][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.069][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.071][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.078][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:16.080][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:16.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.083][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.085][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:16.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:16.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.090][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:16.092][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:16.093][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.094][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.096][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:16.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:16.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.103][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:16.104][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:16.106][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.107][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:16.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:16.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.116][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:16.118][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:16.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.120][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:16.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:16.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.129][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:16.131][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:16.132][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.133][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.135][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:16.137][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:16.138][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.139][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.141][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:16.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:16.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.146][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:16.147][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:16.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.150][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:16.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:16.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.173][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:16.174][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:16.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.177][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:16.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:16.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.185][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:16.186][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:16.187][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.189][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.191][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:16.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:16.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.198][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:16.200][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:16.201][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.202][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.204][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:16.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:16.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:16.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:16.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:16.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:16.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:16.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:16.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:16.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:16.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:16.283][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-10-17 05:44:16.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:16.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:16.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:16.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:16.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:16.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:16.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:16.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:16.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:16.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:16.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:16.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:16.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:16.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:16.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:16.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:16.327][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-10-17 05:44:16.328][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:16.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-10-17 05:44:16.333][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:16.335][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:16.336][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:16.338][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:16.340][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:16.341][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:16.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:16.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:16.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:16.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:16.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:16.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:16.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:16.367][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-10-17 05:44:16.373][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:16.376][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:16.378][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-10-17 05:44:17.034][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-10-17 05:44:17.630][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:17.633][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-10-17 05:44:17.641][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-10-17 05:44:17.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-10-17 05:44:17.648][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:17.654][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:17.655][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:17.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:17.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:17.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:17.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:17.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:17.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:17.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:17.685][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.686][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.692][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.704][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:17.728][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:17.729][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.733][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.736][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:17.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:17.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.747][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:17.748][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:17.752][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.754][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:17.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:17.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.770][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:17.772][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:17.773][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.777][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:17.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:17.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.786][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:17.790][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:17.791][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.792][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:17.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:17.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.801][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:17.803][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:17.808][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.809][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.810][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:17.816][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:17.818][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.819][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.821][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:17.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:17.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.830][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:17.832][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:17.833][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.835][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:17.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:17.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.846][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:17.847][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:17.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.853][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:17.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:17.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.865][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:17.866][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:17.867][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.869][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.870][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:17.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:17.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.881][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:17.882][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:17.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.884][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.888][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:17.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:17.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:17.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:17.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:17.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:17.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:17.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:17.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:17.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:17.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:17.979][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-10-17 05:44:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:17.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:17.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:17.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:17.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:17.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:17.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:18.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:18.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:18.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:18.045][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[2023-10-17 05:44:18.063][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:18.066][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:18.072][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:18.732][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:19.571][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:19.574][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-10-17 05:44:19.579][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-10-17 05:44:19.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:19.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:19.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:19.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:19.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:19.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:19.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:19.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:19.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:19.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:19.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:19.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:19.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:19.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:19.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:19.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:19.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:19.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:19.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:19.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:19.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:19.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:19.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:19.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:19.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:19.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:19.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:19.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:19.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:19.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:19.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:19.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:19.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:19.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:19.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:19.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:19.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:19.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:19.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:19.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:19.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:19.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:19.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:19.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:19.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:19.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:19.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:19.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:19.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:19.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:19.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:19.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:19.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:19.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:19.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:19.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:19.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:19.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:19.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:19.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:19.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:19.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:19.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:19.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:19.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:19.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:19.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:20.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:20.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:20.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:20.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:20.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:20.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:20.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:20.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:20.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:20.620][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:20.628][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:20.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:20.632][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:21.185][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:21.875][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:21.881][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-10-17 05:44:21.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-10-17 05:44:21.896][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[2023-10-17 05:44:21.900][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:21.905][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:21.908][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:22.583][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:23.265][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:23.269][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-10-17 05:44:23.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-10-17 05:44:23.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:23.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:23.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:23.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:23.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:23.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:23.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:23.304][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-10-17 05:44:23.307][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:23.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-10-17 05:44:23.314][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:23.315][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:23.318][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:23.319][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:23.321][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:23.326][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:23.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:23.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:23.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:23.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:23.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:23.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:23.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:23.354][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-10-17 05:44:23.360][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:23.363][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:23.366][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-10-17 05:44:24.117][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-10-17 05:44:24.841][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:24.846][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-10-17 05:44:24.852][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-10-17 05:44:24.859][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-10-17 05:44:24.864][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:24.865][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:24.870][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:24.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:24.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:24.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:24.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:24.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:24.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:24.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:24.935][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:24.938][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:24.940][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:24.941][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:24.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:24.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:24.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:24.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:24.953][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:24.958][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:24.959][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:24.963][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:24.965][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:24.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:24.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:24.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:24.972][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:24.977][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:24.978][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:24.983][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:24.987][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:24.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:24.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:24.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:24.996][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:24.997][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:24.999][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.000][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:25.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:25.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.012][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:25.014][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:25.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.017][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:25.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:25.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.031][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:25.036][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:25.037][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.038][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.041][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:25.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:25.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.051][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:25.053][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:25.054][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.057][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.058][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:25.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:25.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.066][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.070][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.072][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.073][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.085][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:25.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:25.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.095][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:25.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:25.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.108][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:25.110][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:25.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.116][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.118][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:25.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:25.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.128][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:25.129][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:25.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.133][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.134][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:25.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:25.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:25.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:25.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:25.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:25.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:25.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:25.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:25.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:25.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:25.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:25.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:25.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:25.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:25.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:25.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:25.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:25.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:25.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:25.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:25.220][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-10-17 05:44:25.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:25.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:25.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:25.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:25.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:25.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:25.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:25.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:25.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:25.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:25.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:25.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:25.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:25.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:25.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:25.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:25.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:25.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:25.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:25.337][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-10-17 05:44:25.339][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:25.341][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-10-17 05:44:25.346][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:25.347][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:25.350][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:25.353][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:25.355][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:25.358][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:25.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:25.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:25.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:25.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:25.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:25.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:25.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:25.386][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-10-17 05:44:25.393][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:25.394][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:25.396][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-10-17 05:44:25.997][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-10-17 05:44:26.565][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:26.568][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-10-17 05:44:26.574][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-10-17 05:44:26.579][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-10-17 05:44:26.583][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:26.585][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:26.587][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:26.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:26.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:26.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:26.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:26.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:26.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:26.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:26.613][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.615][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.618][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.626][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:26.629][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:26.630][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.631][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.635][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:26.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:26.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.643][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:26.645][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:26.648][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.650][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.651][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:26.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:26.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.660][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:26.662][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:26.664][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.665][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:26.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:26.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.675][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:26.676][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:26.678][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.680][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:26.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:26.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.689][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:26.691][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:26.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.696][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.697][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:26.701][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:26.702][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.703][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.706][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:26.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:26.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.714][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.716][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.728][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:26.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:26.731][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.734][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:26.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:26.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.765][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:26.766][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:26.768][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.770][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.771][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:26.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:26.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:26.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:26.785][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.789][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:26.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:26.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:26.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:26.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:26.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:26.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:26.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:26.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:26.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:26.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:26.877][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-10-17 05:44:26.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:26.941][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:26.946][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:26.948][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-10-17 05:44:26.950][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:26.956][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-10-17 05:44:26.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:26.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:26.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:26.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:26.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:26.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:26.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:26.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:26.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:26.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:26.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.904][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:27.910][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:27.912][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-10-17 05:44:27.915][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:27.920][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-10-17 05:44:27.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:27.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:27.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:27.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:27.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:27.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:27.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:27.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:27.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:27.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:27.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:27.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:28.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.818][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-17 05:44:28.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-17 05:44:28.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:44:28.844][biodb::testThat]
biodb.INFO [2023-10-17 05:44:28.847][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-10-17 05:44:28.849][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:28.851][biodb::testThat]
biodb.TRACE[2023-10-17 05:44:28.857][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-17 05:44:28.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-17 05:44:28.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:28.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:28.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:28.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:28.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:28.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:28.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:28.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:28.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:28.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:28.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:28.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:28.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:28.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:28.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:28.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:28.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:28.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:28.945][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:28.952][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:28.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:28.957][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:29.618][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:30.301][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:30.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-10-17 05:44:30.313][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-10-17 05:44:30.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:30.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:30.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:30.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:30.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:30.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:30.343][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.TRACE[2023-10-17 05:44:30.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:30.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:30.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:30.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:30.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:30.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:30.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:30.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:30.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:30.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:30.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:30.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:30.369][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[2023-10-17 05:44:30.375][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:30.376][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:30.379][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:31.012][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:31.665][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:31.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-10-17 05:44:31.674][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-10-17 05:44:31.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:31.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:31.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:31.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:31.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:31.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:31.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:31.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:31.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:31.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:31.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:31.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:31.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:31.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:31.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:31.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:31.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:31.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:31.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:31.733][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:31.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:31.741][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:31.745][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:32.295][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:32.978][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:32.981][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-10-17 05:44:32.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-10-17 05:44:32.995][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:44:32.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:33.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:33.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:33.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:33.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:33.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:33.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:33.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.039][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:33.040][private$selectFields]
biodb.TRACE[2023-10-17 05:44:33.042][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:33.044][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:33.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:33.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.054][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.060][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.062][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.063][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:33.066][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:33.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.069][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.070][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.073][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.074][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:33.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.149][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-10-17 05:44:33.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:33.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:33.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:33.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:33.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:33.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:33.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:33.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.184][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:33.185][private$selectFields]
biodb.TRACE[2023-10-17 05:44:33.186][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:33.191][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:33.192][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:33.197][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.200][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.203][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.204][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.210][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.211][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.212][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:33.216][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:33.217][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.218][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.223][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.224][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:33.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:33.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.254][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-10-17 05:44:33.255][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:44:33.260][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:44:33.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:33.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:33.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:33.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:33.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:33.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:33.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:33.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:33.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:33.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:33.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:33.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:33.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:33.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:33.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:33.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:33.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:33.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:33.452][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:33.457][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:33.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:33.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:34.145][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:34.874][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:34.878][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-10-17 05:44:34.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-10-17 05:44:34.892][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[2023-10-17 05:44:34.897][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:34.899][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:34.901][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:35.532][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:36.222][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:36.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-10-17 05:44:36.235][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-10-17 05:44:36.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:36.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:36.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:36.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:36.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:36.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:36.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:36.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:36.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:36.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:36.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:36.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:36.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:36.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:36.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:36.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:36.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:36.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:36.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:36.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:36.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:36.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:36.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:36.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:36.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:36.448][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:44:36.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:36.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:36.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:36.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:36.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:36.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:36.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:36.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.532][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.534][private$selectFields]
biodb.TRACE[2023-10-17 05:44:36.535][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:36.536][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:36.538][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.539][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.545][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.546][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.549][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.550][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.551][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.552][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.557][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.558][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.559][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.561][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.563][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.564][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.568][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:36.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.594][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-10-17 05:44:36.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:36.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:36.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:36.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:36.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:36.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:36.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:36.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.689][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.691][private$selectFields]
biodb.TRACE[2023-10-17 05:44:36.692][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:36.694][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:36.709][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.714][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.720][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.721][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.723][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.727][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.728][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.729][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.732][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.752][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.753][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.755][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.757][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.758][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.759][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:36.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.783][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-10-17 05:44:36.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:36.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:36.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:36.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:36.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:36.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:36.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:36.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.822][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.824][private$selectFields]
biodb.TRACE[2023-10-17 05:44:36.825][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:36.826][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:36.831][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.834][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.835][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.836][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.838][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.844][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.845][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.846][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.848][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:36.849][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.850][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.855][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.857][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.858][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:36.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:36.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.884][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-10-17 05:44:36.885][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:44:36.887][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:44:36.900][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-17 05:44:36.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-17 05:44:36.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:44:36.917][biodb::testThat]
biodb.INFO [2023-10-17 05:44:36.919][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-10-17 05:44:36.921][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:36.922][biodb::testThat]
biodb.TRACE[2023-10-17 05:44:36.929][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-17 05:44:36.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-17 05:44:36.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:36.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:36.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:36.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:36.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:36.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:36.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:36.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:36.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:36.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:36.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:36.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:36.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:36.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:36.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:36.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:36.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:36.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:36.996][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:37.015][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:37.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-10-17 05:44:37.022][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:37.026][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-10-17 05:44:37.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:37.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:37.078][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:37.085][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:37.090][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-10-17 05:44:37.092][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:37.097][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-10-17 05:44:37.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:37.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:37.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:37.152][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:37.158][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:37.161][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-10-17 05:44:37.165][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:37.171][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-10-17 05:44:37.174][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:44:37.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:37.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.222][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.224][private$selectFields]
biodb.TRACE[2023-10-17 05:44:37.228][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:37.230][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:37.233][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.235][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.241][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.244][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.246][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.254][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.256][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.258][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.259][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.268][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.275][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.276][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:37.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.307][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-10-17 05:44:37.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.331][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.TRACE[2023-10-17 05:44:37.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.353][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.355][private$selectFields]
biodb.TRACE[2023-10-17 05:44:37.356][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:37.360][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:37.362][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.363][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.366][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.367][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.385][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.387][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.392][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.397][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.400][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.402][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.404][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.411][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.412][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.415][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:37.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.446][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-10-17 05:44:37.447][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:44:37.449][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:44:37.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:37.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:37.525][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[2023-10-17 05:44:37.530][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:37.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-10-17 05:44:37.536][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:37.540][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-10-17 05:44:37.545][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[2023-10-17 05:44:37.549][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:37.551][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-10-17 05:44:37.553][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:37.555][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-10-17 05:44:37.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:37.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:37.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:37.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:37.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.663][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[2023-10-17 05:44:37.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:37.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:37.698][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:44:37.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.740][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.TRACE[2023-10-17 05:44:37.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.761][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.764][private$selectFields]
biodb.TRACE[2023-10-17 05:44:37.765][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:37.766][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:37.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.771][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.778][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.782][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.785][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.787][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.789][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.790][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.796][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.800][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.802][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:37.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.827][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-10-17 05:44:37.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:37.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.870][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.871][private$selectFields]
biodb.TRACE[2023-10-17 05:44:37.872][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:37.876][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:37.878][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.879][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.883][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.884][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.886][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.891][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.893][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.896][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.898][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.902][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.906][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.909][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.910][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.911][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:37.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.941][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-10-17 05:44:37.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:37.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:37.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:37.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:37.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:37.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:37.963][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[2023-10-17 05:44:37.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:37.981][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.983][private$selectFields]
biodb.TRACE[2023-10-17 05:44:37.984][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:37.987][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:37.988][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:37.994][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.996][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:37.997][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:37.999][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.005][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.007][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.008][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.009][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.010][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.011][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.018][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.020][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.021][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:38.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.067][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-10-17 05:44:38.068][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:44:38.069][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:44:38.088][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-17 05:44:38.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-17 05:44:38.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:44:38.102][biodb::testThat]
biodb.INFO [2023-10-17 05:44:38.107][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-10-17 05:44:38.108][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:38.109][biodb::testThat]
biodb.TRACE[2023-10-17 05:44:38.115][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-10-17 05:44:38.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-10-17 05:44:38.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:38.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:38.195][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[2023-10-17 05:44:38.199][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:38.201][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-10-17 05:44:38.203][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:38.209][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-10-17 05:44:38.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:38.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:38.251][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[2023-10-17 05:44:38.258][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:38.261][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-10-17 05:44:38.263][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:38.265][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-10-17 05:44:38.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:38.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:38.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:38.314][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:38.319][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:38.320][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-10-17 05:44:38.322][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:38.326][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-10-17 05:44:38.330][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:44:38.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.350][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[2023-10-17 05:44:38.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.380][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.382][private$selectFields]
biodb.TRACE[2023-10-17 05:44:38.383][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:38.384][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:38.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.395][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.396][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.399][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.401][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.402][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.404][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.406][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.407][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.408][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.410][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.411][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:38.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.443][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-10-17 05:44:38.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:38.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.479][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.480][private$selectFields]
biodb.TRACE[2023-10-17 05:44:38.481][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:38.483][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:38.484][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.486][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.487][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.490][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.491][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.493][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.495][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.498][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.501][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.506][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.509][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.511][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:38.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.538][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-10-17 05:44:38.540][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:44:38.541][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:44:38.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:38.610][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:38.627][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:38.631][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:38.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-10-17 05:44:38.634][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:38.639][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-10-17 05:44:38.658][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:38.665][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:38.666][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-10-17 05:44:38.671][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:38.673][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-10-17 05:44:38.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:38.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:38.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:38.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:38.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:38.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:38.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:38.804][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-10-17 05:44:38.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:38.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.839][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.841][private$selectFields]
biodb.TRACE[2023-10-17 05:44:38.842][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:38.846][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:38.847][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.848][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.851][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.852][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.855][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.856][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.858][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.860][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.862][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.864][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.866][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.867][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.870][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.871][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.873][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.876][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:38.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.898][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-10-17 05:44:38.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:38.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:38.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:38.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:38.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:38.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:38.920][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.TRACE[2023-10-17 05:44:38.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.952][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.954][private$selectFields]
biodb.TRACE[2023-10-17 05:44:38.955][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:38.956][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:38.961][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.962][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.963][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.966][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.967][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.971][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.973][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.975][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.981][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:38.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.983][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.985][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.986][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.988][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:38.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:38.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:38.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:38.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.012][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-10-17 05:44:39.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:39.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:39.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:39.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:39.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:39.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:39.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:39.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.051][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:39.054][private$selectFields]
biodb.TRACE[2023-10-17 05:44:39.058][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-10-17 05:44:39.059][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-10-17 05:44:39.060][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:39.062][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.065][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.067][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.070][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.072][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.074][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.075][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:39.079][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-10-17 05:44:39.080][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.081][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.084][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.085][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-10-17 05:44:39.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:39.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:39.114][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-10-17 05:44:39.116][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-10-17 05:44:39.118][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-10-17 05:44:39.149][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-10-17 05:44:39.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-10-17 05:44:39.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:39.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-17 05:44:39.167][biodb::testThat]
biodb.INFO [2023-10-17 05:44:39.169][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-10-17 05:44:39.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:39.174][biodb::testThat]
biodb.DEBUG[2023-10-17 05:44:39.179][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-10-17 05:44:39.181][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:44:39.185][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-10-17 05:44:39.187][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:44:39.190][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:39.192][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:39.194][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:39.196][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:39.199][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:39.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:39.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:39.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:39.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:39.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:39.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:39.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:39.226][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-10-17 05:44:39.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:39.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:39.234][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-10-17 05:44:39.924][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-10-17 05:44:40.601][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:40.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-10-17 05:44:40.612][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-10-17 05:44:40.617][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-10-17 05:44:40.619][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:40.621][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:44:40.622][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:40.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:40.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:40.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:40.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:40.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:40.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:40.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:40.649][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.651][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.654][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.656][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.665][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:40.666][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:40.668][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.669][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.670][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:40.674][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:40.675][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.676][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.678][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:40.680][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:40.681][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.685][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.687][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:40.688][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:40.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.691][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.694][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:40.696][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:40.697][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.699][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.701][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:40.704][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:40.706][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.708][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.710][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:40.711][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:40.715][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.717][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.719][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:40.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:40.722][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.723][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.725][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:40.726][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:40.728][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.729][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.731][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:40.734][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:40.736][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.740][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:40.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:40.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:40.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:40.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:40.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:40.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:40.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:40.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:40.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:40.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:40.815][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-10-17 05:44:40.816][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-10-17 05:44:40.829][biodb::testThat]
biodb.INFO [2023-10-17 05:44:40.831][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-10-17 05:44:40.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:40.835][biodb::testThat]
biodb.DEBUG[2023-10-17 05:44:40.849][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-10-17 05:44:40.851][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-10-17 05:44:40.852][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-10-17 05:44:40.854][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-10-17 05:44:40.857][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-10-17 05:44:40.858][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:44:40.860][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:44:40.862][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:40.864][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:44:40.865][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:44:40.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:40.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:40.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:40.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:40.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:40.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:40.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:40.913][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-10-17 05:44:40.918][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:40.920][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:40.922][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-10-17 05:44:41.692][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-10-17 05:44:42.417][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:42.420][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-10-17 05:44:42.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-10-17 05:44:42.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:42.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:42.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:42.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:42.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:42.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:42.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:42.452][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-10-17 05:44:42.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:42.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:42.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-10-17 05:44:43.044][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-10-17 05:44:43.602][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:43.607][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-10-17 05:44:43.613][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-10-17 05:44:43.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:43.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:43.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:43.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:43.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:43.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:43.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:43.632][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-10-17 05:44:43.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:43.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:43.641][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-10-17 05:44:44.305][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-10-17 05:44:45.036][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:45.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-10-17 05:44:45.046][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-10-17 05:44:45.051][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2023-10-17 05:44:45.055][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:44:45.057][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-10-17 05:44:45.059][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-10-17 05:44:45.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:45.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:45.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:45.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:45.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:45.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:45.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:45.080][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.084][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.085][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.087][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.100][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:45.102][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:45.103][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.104][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.106][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:45.108][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:45.110][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.111][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.113][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:45.115][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:45.117][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.118][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.120][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.121][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.123][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.125][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.126][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.130][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.132][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.134][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.136][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:45.137][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:45.140][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.141][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.144][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.146][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.148][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.149][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.151][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:45.154][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:45.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.157][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.162][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:45.163][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:45.164][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.166][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.167][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:45.169][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:45.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.172][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:45.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:45.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:45.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:45.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:45.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:45.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:45.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:45.271][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.273][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.277][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.288][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:45.289][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:45.291][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.295][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.297][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:45.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:45.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.307][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:45.309][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:45.311][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.313][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:45.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:45.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.325][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:45.327][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:45.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.331][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:45.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:45.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.343][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.345][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.346][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.347][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.356][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.359][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.361][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.362][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.366][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.373][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:45.376][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:45.377][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.378][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.381][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:45.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:45.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.390][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.392][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.393][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.395][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.404][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:45.406][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:45.407][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.410][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:45.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:45.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.419][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:45.421][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:45.422][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.425][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.427][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:45.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:45.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.435][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:45.436][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:45.437][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.438][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.440][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:45.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:45.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:45.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:45.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:45.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:45.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:45.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:45.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:45.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:44:45.533][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.535][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.536][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.537][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.546][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:45.547][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:45.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.549][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.552][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:44:45.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:44:45.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.559][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:45.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:45.561][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.563][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:44:45.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:44:45.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.574][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:45.575][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:45.577][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.581][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:44:45.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:44:45.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.589][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.590][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.594][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:44:45.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.604][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.606][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.607][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.610][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.612][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:44:45.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.621][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:45.623][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:45.625][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.627][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.628][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:44:45.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:44:45.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.635][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.637][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.638][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.642][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:45.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.651][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:45.652][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:45.653][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.656][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:45.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:45.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.665][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:45.667][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:45.669][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.671][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.673][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:44:45.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:44:45.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.680][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:45.683][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:45.684][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.686][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.688][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:44:45.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:44:45.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:44:45.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:45.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:44:45.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:44:45.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:45.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:44:45.833][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-10-17 05:44:45.835][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-10-17 05:44:45.836][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-10-17 05:44:45.862][biodb::testThat]
biodb.INFO [2023-10-17 05:44:45.863][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-10-17 05:44:45.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:45.868][biodb::testThat]
biodb.INFO [2023-10-17 05:44:45.908][biodb::testThat]
biodb.INFO [2023-10-17 05:44:45.909][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-10-17 05:44:45.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:45.913][biodb::testThat]
biodb.INFO [2023-10-17 05:44:45.929][biodb::testThat]
biodb.INFO [2023-10-17 05:44:45.930][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-10-17 05:44:45.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:45.932][biodb::testThat]
biodb.DEBUG[2023-10-17 05:44:45.939][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:45.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:45.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:45.948][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:46.816][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:47.635][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:47.638][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-10-17 05:44:47.647][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-10-17 05:44:47.668][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:44:47.673][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:44:47.674][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:47.678][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:44:47.680][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:47.682][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:44:47.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:44:47.688][ef$get] fields variable is a list.
biodb.INFO [2023-10-17 05:44:47.692][biodb::testThat]
biodb.INFO [2023-10-17 05:44:47.693][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-10-17 05:44:47.697][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:47.699][biodb::testThat]
biodb.ERROR[2023-10-17 05:44:47.720][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-10-17 05:44:47.763][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-10-17 05:44:47.785][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-17 05:44:47.790][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-10-17 05:44:47.792][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-10-17 05:44:47.794][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-17 05:44:47.796][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:47.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:47.800][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:47.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:47.802][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.805][FUN] Functions in observer BiodbConfig: [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 [2023-10-17 05:44:47.820][biodb::testContext]
biodb.INFO [2023-10-17 05:44:47.822][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:44:47.823][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-10-17 05:44:47.824][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:44:47.825][biodb::testContext]
biodb.INFO [2023-10-17 05:44:47.830][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:44:47.833][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-17 05:44:47.839][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:44:47.840][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-17 05:44:47.844][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-17 05:44:47.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.852][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-17 05:44:47.853][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-17 05:44:47.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.859][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-17 05:44:47.860][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-17 05:44:47.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.868][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-17 05:44:47.870][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-17 05:44:47.872][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-17 05:44:47.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.877][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-17 05:44:47.882][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-17 05:44:47.884][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-17 05:44:47.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.889][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-17 05:44:47.894][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-17 05:44:47.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.897][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[2023-10-17 05:44:47.899][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-17 05:44:47.901][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-17 05:44:47.904][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-17 05:44:47.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.909][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-17 05:44:47.910][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-17 05:44:47.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.919][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-17 05:44:47.920][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-17 05:44:47.922][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-17 05:44:47.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.932][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:44:47.933][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-17 05:44:47.934][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-17 05:44:47.935][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-17 05:44:47.937][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-17 05:44:47.939][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-17 05:44:47.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.948][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[2023-10-17 05:44:47.950][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-17 05:44:47.952][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-17 05:44:47.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.957][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-17 05:44:47.958][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-17 05:44:47.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.966][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-17 05:44:47.969][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-17 05:44:47.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.977][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-17 05:44:47.978][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-17 05:44:47.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.984][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-17 05:44:47.985][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-17 05:44:47.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:47.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:47.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:47.991][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:44:47.992][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-17 05:44:48.018][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-17 05:44:48.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.025][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-17 05:44:48.026][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-17 05:44:48.028][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-17 05:44:48.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.036][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-17 05:44:48.040][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.041][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-17 05:44:48.044][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.046][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:48.047][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.274][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.276][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.278][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.282][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:44:48.283][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:48.285][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.288][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-17 05:44:48.289][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:48.293][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.294][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.296][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:44:48.296][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:44:48.296][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:44:48.296][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:44:48.296][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:44:48.298][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:44:48.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:48.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:48.305][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:48.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:48.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:48.311][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.313][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.314][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:48.315][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:48.316][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.320][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.321][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-17 05:44:48.324][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.325][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:44:48.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:48.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.333][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.334][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.336][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.339][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:44:48.341][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:48.343][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.345][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-17 05:44:48.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:48.350][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.351][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.352][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:44:48.352][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:44:48.352][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:44:48.352][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:44:48.352][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:44:48.355][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:44:48.356][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:48.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:48.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:48.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:48.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:48.365][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.366][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.367][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:48.370][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:48.371][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.372][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.375][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-17 05:44:48.377][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.380][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-17 05:44:48.382][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.383][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:48.385][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.387][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.388][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.389][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.390][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:44:48.392][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:48.394][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.395][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-17 05:44:48.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:48.401][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.403][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.404][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.405][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:44:48.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:48.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:48.411][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:48.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:48.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:48.418][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.420][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.421][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:48.422][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:48.425][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.426][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.428][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-17 05:44:48.430][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.431][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:44:48.435][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.436][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:48.438][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.439][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.441][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.442][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.443][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:44:48.446][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:48.447][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.448][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-17 05:44:48.452][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:48.453][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.454][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:48.456][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.457][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:44:48.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:48.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:48.462][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:48.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:48.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:48.465][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:48.466][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.468][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:48.469][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:48.472][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:48.473][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:48.477][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:44:48.478][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.479][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.DEBUG[2023-10-17 05:44:48.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.498][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[2023-10-17 05:44:48.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.505][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[2023-10-17 05:44:48.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.530][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[2023-10-17 05:44:48.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.547][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[2023-10-17 05:44:48.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.566][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[2023-10-17 05:44:48.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.583][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[2023-10-17 05:44:48.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.595][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[2023-10-17 05:44:48.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.614][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[2023-10-17 05:44:48.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.636][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-17 05:44:48.638][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-17 05:44:48.643][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-17 05:44:48.647][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-17 05:44:48.649][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:44:48.653][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-17 05:44:48.657][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-17 05:44:48.659][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-17 05:44:48.662][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-17 05:44:48.665][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-17 05:44:48.667][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:44:48.669][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-17 05:44:48.672][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-17 05:44:48.674][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-17 05:44:48.677][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-17 05:44:48.679][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:44:48.682][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-17 05:44:48.685][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-17 05:44:48.687][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:44:48.689][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-17 05:44:48.693][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-17 05:44:48.695][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-17 05:44:48.698][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-17 05:44:48.700][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-17 05:44:48.703][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-17 05:44:48.705][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-17 05:44:48.708][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-17 05:44:48.710][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-17 05:44:48.713][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-17 05:44:48.718][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-17 05:44:48.720][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-17 05:44:48.723][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-17 05:44:48.725][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-17 05:44:48.728][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-17 05:44:48.732][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-17 05:44:48.736][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-17 05:44:48.738][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-17 05:44:48.742][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-17 05:44:48.745][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-17 05:44:48.748][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-17 05:44:48.751][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-17 05:44:48.753][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-17 05:44:48.757][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-17 05:44:48.759][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-17 05:44:48.763][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-17 05:44:48.768][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-17 05:44:48.772][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-17 05:44:48.775][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-17 05:44:48.779][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-17 05:44:48.781][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-17 05:44:48.786][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-17 05:44:48.789][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-17 05:44:48.792][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-17 05:44:48.796][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-17 05:44:48.798][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-17 05:44:48.802][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-17 05:44:48.805][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-17 05:44:48.807][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-17 05:44:48.811][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-17 05:44:48.813][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-17 05:44:48.818][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-17 05:44:48.820][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-17 05:44:48.823][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-17 05:44:48.825][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-17 05:44:48.828][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-17 05:44:48.830][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-17 05:44:48.835][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:44:48.838][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:44:48.841][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-17 05:44:48.844][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-17 05:44:48.846][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-17 05:44:48.851][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-17 05:44:48.856][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-17 05:44:48.858][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-17 05:44:48.860][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-17 05:44:48.863][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-17 05:44:48.867][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-17 05:44:48.881][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-17 05:44:48.883][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-17 05:44:48.884][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-17 05:44:48.888][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-17 05:44:48.890][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-17 05:44:48.892][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-17 05:44:48.894][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-17 05:44:48.898][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:44:48.900][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:44:48.901][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.904][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.905][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[2023-10-17 05:44:48.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:48.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:48.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:48.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:48.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:48.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:48.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.942][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[2023-10-17 05:44:48.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:48.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:48.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:48.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:48.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:48.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:48.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:48.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:48.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:48.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:48.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:48.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:48.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:48.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:48.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:48.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:49.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:49.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:49.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:49.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:49.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:49.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:49.105][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-10-17 05:44:49.107][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-10-17 05:44:49.110][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:49.111][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-17 05:44:49.113][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:49.115][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:49.116][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:49.117][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:49.120][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:49.121][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-10-17 05:44:49.122][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-10-17 05:44:49.125][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:49.126][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:49.127][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-10-17 05:44:49.130][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-10-17 05:44:49.131][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-10-17 05:44:49.133][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:49.135][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:44:49.135][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:44:49.135][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:44:49.137][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-17 05:44:49.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:49.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:49.143][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:49.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:49.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:49.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:49.148][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:49.148][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-10-17 05:44:49.151][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:49.152][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:49.153][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:49.154][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-10-17 05:44:49.154][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-10-17 05:44:49.159][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:44:49.163][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:44:49.165][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-10-17 05:44:49.167][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:44:49.169][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:44:49.174][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:44:49.180][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-10-17 05:44:49.181][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-10-17 05:44:49.184][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-10-17 05:44:49.186][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-10-17 05:44:49.188][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-17 05:44:49.189][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-17 05:44:49.191][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-10-17 05:44:49.193][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-10-17 05:44:49.195][biodb::testThat]
biodb.INFO [2023-10-17 05:44:49.199][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2023-10-17 05:44:49.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:49.202][biodb::testThat]
biodb.DEBUG[2023-10-17 05:44:49.207][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-10-17 05:44:49.216][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:49.217][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:49.218][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-10-17 05:44:49.997][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-10-17 05:44:50.635][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:50.638][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-10-17 05:44:50.645][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-10-17 05:44:50.653][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:50.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:50.659][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:50.664][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:51.209][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:51.866][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:51.869][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-10-17 05:44:51.875][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-10-17 05:44:51.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:51.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:51.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:51.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:51.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:51.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:51.896][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[2023-10-17 05:44:51.899][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[2023-10-17 05:44:51.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:51.907][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:51.910][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:52.455][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:53.125][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:53.128][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-10-17 05:44:53.137][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-10-17 05:44:53.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:53.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:53.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:53.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:53.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:53.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:53.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:53.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:53.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:53.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:53.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:53.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:53.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:53.200][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[2023-10-17 05:44:53.210][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:53.215][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:53.217][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-10-17 05:44:53.220][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:53.223][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-10-17 05:44:53.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:53.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:53.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:53.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:53.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:53.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:53.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:53.273][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:53.279][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:53.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-10-17 05:44:53.283][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:53.285][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-10-17 05:44:53.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:53.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:53.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:53.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:53.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:53.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:53.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:53.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:53.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:53.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:53.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:53.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:53.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:53.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:53.339][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:53.344][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:53.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-10-17 05:44:53.351][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:53.353][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-10-17 05:44:53.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:53.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:53.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:53.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:53.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:53.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:53.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:53.381][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:53.387][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:53.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-10-17 05:44:53.394][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:53.396][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-10-17 05:44:53.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:53.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:53.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:53.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:53.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:53.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:53.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:53.419][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:53.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:53.425][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:53.427][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:53.978][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:54.642][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:54.647][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-10-17 05:44:54.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-10-17 05:44:54.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:54.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:54.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:54.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:54.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:54.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:54.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-17 05:44:54.688][biodb::testThat]
biodb.INFO [2023-10-17 05:44:54.689][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2023-10-17 05:44:54.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:54.694][biodb::testThat]
biodb.DEBUG[2023-10-17 05:44:54.699][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[2023-10-17 05:44:54.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:54.708][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:54.713][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:55.523][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:56.051][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:56.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-10-17 05:44:56.063][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-10-17 05:44:56.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:56.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:56.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:56.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:56.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:56.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:56.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:56.089][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:44:56.093][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:56.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:56.101][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:56.681][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:44:57.513][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:44:57.516][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-10-17 05:44:57.524][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-10-17 05:44:57.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:44:57.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:57.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:57.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:57.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:57.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-17 05:44:57.560][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-17 05:44:57.562][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-10-17 05:44:57.564][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-10-17 05:44:57.565][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-17 05:44:57.567][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:57.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:57.570][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:57.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:57.576][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-17 05:44:57.585][biodb::testContext]
biodb.INFO [2023-10-17 05:44:57.588][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:44:57.589][biodb::testContext] Test context - Test web services
biodb.INFO [2023-10-17 05:44:57.591][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:44:57.593][biodb::testContext]
biodb.INFO [2023-10-17 05:44:57.599][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:44:57.602][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-17 05:44:57.608][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:44:57.610][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-17 05:44:57.613][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-17 05:44:57.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.621][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-17 05:44:57.623][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-17 05:44:57.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.630][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-17 05:44:57.634][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-17 05:44:57.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.645][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-17 05:44:57.647][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-17 05:44:57.653][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-17 05:44:57.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.661][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-17 05:44:57.663][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-17 05:44:57.666][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-17 05:44:57.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.671][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-17 05:44:57.673][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-17 05:44:57.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.679][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-17 05:44:57.680][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-17 05:44:57.682][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-17 05:44:57.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.691][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-17 05:44:57.693][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-17 05:44:57.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.699][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-17 05:44:57.700][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-17 05:44:57.701][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-17 05:44:57.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.713][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:44:57.714][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-17 05:44:57.716][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-17 05:44:57.719][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-17 05:44:57.721][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-17 05:44:57.723][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-17 05:44:57.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.730][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-17 05:44:57.732][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-17 05:44:57.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.738][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-17 05:44:57.740][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-17 05:44:57.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.746][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-17 05:44:57.748][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-17 05:44:57.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.756][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-17 05:44:57.759][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-17 05:44:57.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.765][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.DEBUG[2023-10-17 05:44:57.766][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-17 05:44:57.768][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-17 05:44:57.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.775][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:44:57.777][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-17 05:44:57.804][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-17 05:44:57.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.809][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[2023-10-17 05:44:57.811][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-17 05:44:57.815][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-17 05:44:57.816][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-17 05:44:57.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:57.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:57.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:57.825][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-17 05:44:57.828][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:57.830][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-17 05:44:57.832][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.835][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:57.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.839][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:57.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:57.845][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:44:57.870][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:44:57.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:57.875][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.877][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-17 05:44:57.879][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:57.881][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:57.882][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.886][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:44:57.886][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:44:57.886][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:44:57.886][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:44:57.886][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:44:57.888][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:44:57.889][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:57.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:57.893][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:57.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:57.897][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:57.898][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:57.900][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:57.901][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:57.903][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:57.906][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:57.908][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:57.909][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-17 05:44:57.912][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:57.914][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:44:57.916][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.917][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:57.919][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.922][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:57.924][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:57.925][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:44:57.928][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:44:57.929][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:57.932][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.934][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-17 05:44:57.935][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:57.939][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:57.941][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.942][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:44:57.942][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:44:57.942][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:44:57.942][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:44:57.942][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:44:57.943][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:44:57.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:57.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:57.948][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:57.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:57.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:57.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:57.957][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:57.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:57.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:57.965][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:57.968][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:57.970][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-17 05:44:57.975][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.976][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-17 05:44:57.978][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:57.981][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:57.984][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:57.986][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:57.987][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:44:57.990][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:44:57.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:57.993][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:57.997][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-17 05:44:57.998][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:58.000][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:58.003][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.004][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:58.008][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:44:58.009][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:58.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:58.013][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:58.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:58.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:58.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:58.022][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:58.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:58.027][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:58.029][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:58.031][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:58.034][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-17 05:44:58.037][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.042][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:44:58.044][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.046][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:58.048][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:58.054][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:58.055][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:44:58.057][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:44:58.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:58.064][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:58.066][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-17 05:44:58.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:58.072][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:58.074][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.079][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:58.080][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:44:58.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:58.085][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:58.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:58.090][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:58.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:58.094][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:58.100][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:58.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:58.104][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:58.105][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:58.107][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:44:58.110][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:44:58.111][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.112][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[2023-10-17 05:44:58.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.139][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[2023-10-17 05:44:58.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.148][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[2023-10-17 05:44:58.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.175][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[2023-10-17 05:44:58.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.182][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[2023-10-17 05:44:58.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.199][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[2023-10-17 05:44:58.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.215][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[2023-10-17 05:44:58.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.235][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[2023-10-17 05:44:58.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.242][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[2023-10-17 05:44:58.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.251][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-17 05:44:58.255][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-17 05:44:58.257][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-17 05:44:58.261][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-17 05:44:58.263][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:44:58.265][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-17 05:44:58.269][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-17 05:44:58.271][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-17 05:44:58.273][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-17 05:44:58.278][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-17 05:44:58.280][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:44:58.283][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-17 05:44:58.285][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-17 05:44:58.287][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-17 05:44:58.289][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-17 05:44:58.291][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:44:58.292][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-17 05:44:58.297][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-17 05:44:58.299][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:44:58.302][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-17 05:44:58.304][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-17 05:44:58.306][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-17 05:44:58.308][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-17 05:44:58.310][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-17 05:44:58.312][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-17 05:44:58.316][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-17 05:44:58.318][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-17 05:44:58.322][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-17 05:44:58.324][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-17 05:44:58.329][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-17 05:44:58.331][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-17 05:44:58.335][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-17 05:44:58.337][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-17 05:44:58.340][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-17 05:44:58.341][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-17 05:44:58.343][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-17 05:44:58.345][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-17 05:44:58.349][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-17 05:44:58.351][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-17 05:44:58.356][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-17 05:44:58.358][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-17 05:44:58.360][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-17 05:44:58.362][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-17 05:44:58.364][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-17 05:44:58.366][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-17 05:44:58.367][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-17 05:44:58.369][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-17 05:44:58.371][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-17 05:44:58.375][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-17 05:44:58.376][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-17 05:44:58.380][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-17 05:44:58.382][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-17 05:44:58.384][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-17 05:44:58.386][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-17 05:44:58.388][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-17 05:44:58.391][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-17 05:44:58.393][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-17 05:44:58.397][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-17 05:44:58.399][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-17 05:44:58.403][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-17 05:44:58.404][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-17 05:44:58.407][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-17 05:44:58.409][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-17 05:44:58.414][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-17 05:44:58.415][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-17 05:44:58.418][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-17 05:44:58.420][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:44:58.423][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:44:58.425][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-17 05:44:58.428][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-17 05:44:58.430][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-17 05:44:58.434][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-17 05:44:58.436][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-17 05:44:58.439][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-17 05:44:58.441][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-17 05:44:58.443][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-17 05:44:58.456][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-17 05:44:58.459][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-17 05:44:58.465][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-17 05:44:58.467][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-17 05:44:58.469][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-17 05:44:58.471][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-17 05:44:58.474][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-17 05:44:58.476][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-17 05:44:58.481][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:44:58.482][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:44:58.483][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.487][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.498][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[2023-10-17 05:44:58.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.510][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[2023-10-17 05:44:58.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.536][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[2023-10-17 05:44:58.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.547][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[2023-10-17 05:44:58.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.603][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[2023-10-17 05:44:58.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.625][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.DEBUG[2023-10-17 05:44:58.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.652][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[2023-10-17 05:44:58.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.675][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[2023-10-17 05:44:58.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:44:58.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:44:58.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:44:58.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:44:58.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:44:58.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:44:58.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:44:58.692][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-10-17 05:44:58.693][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-10-17 05:44:58.697][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:58.698][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-17 05:44:58.702][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.704][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:44:58.707][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.709][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:44:58.710][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.714][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-10-17 05:44:58.715][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-10-17 05:44:58.717][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:44:58.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.721][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-10-17 05:44:58.723][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-10-17 05:44:58.724][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-10-17 05:44:58.726][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-17 05:44:58.728][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:44:58.728][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:44:58.728][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:44:58.730][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-17 05:44:58.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:58.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:58.738][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:44:58.740][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:44:58.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:44:58.744][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:44:58.746][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:44:58.746][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-10-17 05:44:58.748][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:44:58.749][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:44:58.750][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-17 05:44:58.752][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-10-17 05:44:58.752][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-10-17 05:44:58.754][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:44:58.756][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:44:58.759][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-10-17 05:44:58.763][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:44:58.765][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:44:58.768][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:44:58.773][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-10-17 05:44:58.774][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-10-17 05:44:58.777][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-10-17 05:44:58.779][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-10-17 05:44:58.781][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-17 05:44:58.783][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-17 05:44:58.784][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-10-17 05:44:58.786][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-10-17 05:44:58.788][biodb::testThat]
biodb.INFO [2023-10-17 05:44:58.789][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-10-17 05:44:58.790][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:44:58.791][biodb::testThat]
biodb.DEBUG[2023-10-17 05:44:58.796][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-10-17 05:44:58.803][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:44:58.805][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-10-17 05:44:58.807][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:44:58.809][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-10-17 05:44:58.814][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[2023-10-17 05:44:58.820][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:44:58.822][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:44:58.824][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-10-17 05:44:59.381][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-10-17 05:45:00.068][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:00.072][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-10-17 05:45:00.078][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-10-17 05:45:00.091][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-17 05:45:00.092][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-10-17 05:45:00.094][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-10-17 05:45:00.095][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-17 05:45:00.096][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:00.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:00.098][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.101][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-17 05:45:00.110][biodb::testContext]
biodb.INFO [2023-10-17 05:45:00.112][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:45:00.114][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-10-17 05:45:00.115][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-17 05:45:00.117][biodb::testContext]
biodb.INFO [2023-10-17 05:45:00.123][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:45:00.126][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-17 05:45:00.131][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:45:00.133][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-17 05:45:00.135][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-17 05:45:00.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.146][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-17 05:45:00.147][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-17 05:45:00.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.152][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-17 05:45:00.155][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-17 05:45:00.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.161][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.DEBUG[2023-10-17 05:45:00.163][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-17 05:45:00.166][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-17 05:45:00.168][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-17 05:45:00.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.173][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-17 05:45:00.178][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-17 05:45:00.180][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-17 05:45:00.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.187][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-17 05:45:00.188][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-17 05:45:00.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.196][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-17 05:45:00.198][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-17 05:45:00.199][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-17 05:45:00.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.204][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-17 05:45:00.205][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-17 05:45:00.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.211][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-17 05:45:00.212][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-17 05:45:00.214][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-17 05:45:00.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.224][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:45:00.226][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-17 05:45:00.228][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-17 05:45:00.230][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-17 05:45:00.232][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-17 05:45:00.234][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-17 05:45:00.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.242][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-17 05:45:00.243][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-17 05:45:00.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.248][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[2023-10-17 05:45:00.250][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-17 05:45:00.253][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-17 05:45:00.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.276][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-17 05:45:00.277][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-17 05:45:00.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.284][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-17 05:45:00.288][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-17 05:45:00.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.296][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-17 05:45:00.298][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-17 05:45:00.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.304][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-17 05:45:00.306][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-17 05:45:00.332][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-17 05:45:00.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.337][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-17 05:45:00.338][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-17 05:45:00.339][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-17 05:45:00.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.346][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-17 05:45:00.348][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.352][self$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[2023-10-17 05:45:00.353][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.354][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:00.356][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.358][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.359][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.363][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.365][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:45:00.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:00.369][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.370][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-17 05:45:00.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:00.373][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.374][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.375][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:45:00.375][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:45:00.375][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:45:00.375][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:45:00.375][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:45:00.377][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:00.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:00.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:00.381][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:00.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:00.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:00.385][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.386][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:00.390][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:00.391][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.393][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.394][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-17 05:45:00.399][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.401][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:45:00.402][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.404][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:00.405][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.406][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.409][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.411][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.414][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:45:00.416][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:00.417][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.420][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-17 05:45:00.421][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:00.423][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.424][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.426][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:45:00.426][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:45:00.426][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:45:00.426][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-17 05:45:00.426][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-17 05:45:00.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:00.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:00.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:00.434][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:00.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:00.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:00.439][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.441][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.442][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:00.443][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:00.445][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.446][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.450][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-17 05:45:00.453][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.454][self$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[2023-10-17 05:45:00.456][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.457][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:00.460][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.461][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.464][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.466][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-17 05:45:00.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:00.473][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.474][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-17 05:45:00.477][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:00.479][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.482][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.484][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.485][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:00.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:00.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:00.490][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:00.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:00.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:00.495][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.496][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.497][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:00.498][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:00.499][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.502][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.504][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-17 05:45:00.509][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.510][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-17 05:45:00.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.514][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:00.515][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.516][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.518][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.520][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.521][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-17 05:45:00.524][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:00.526][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.528][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-17 05:45:00.530][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:00.534][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.536][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:00.539][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.541][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-17 05:45:00.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:00.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:00.545][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:00.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:00.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:00.551][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:00.553][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:00.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:00.559][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:00.560][self$setPropertyValue]
biodb.DEBUG[2023-10-17 05:45:00.562][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:45:00.563][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.564][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[2023-10-17 05:45:00.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.572][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[2023-10-17 05:45:00.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.624][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[2023-10-17 05:45:00.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.661][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[2023-10-17 05:45:00.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.707][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-17 05:45:00.709][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-17 05:45:00.711][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-17 05:45:00.713][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-17 05:45:00.717][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:45:00.721][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-17 05:45:00.723][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-17 05:45:00.728][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-17 05:45:00.730][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-17 05:45:00.732][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-17 05:45:00.734][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:45:00.738][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-17 05:45:00.740][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-17 05:45:00.742][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-17 05:45:00.745][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-17 05:45:00.749][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-17 05:45:00.751][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-17 05:45:00.753][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-17 05:45:00.755][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:45:00.758][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-17 05:45:00.760][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-17 05:45:00.763][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-17 05:45:00.765][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-17 05:45:00.769][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-17 05:45:00.772][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-17 05:45:00.775][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-17 05:45:00.778][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-17 05:45:00.781][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-17 05:45:00.783][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-17 05:45:00.784][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-17 05:45:00.789][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-17 05:45:00.791][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-17 05:45:00.794][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-17 05:45:00.795][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-17 05:45:00.798][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-17 05:45:00.800][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-17 05:45:00.803][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-17 05:45:00.805][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-17 05:45:00.806][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-17 05:45:00.808][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-17 05:45:00.810][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-17 05:45:00.815][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-17 05:45:00.817][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-17 05:45:00.820][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-17 05:45:00.822][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-17 05:45:00.824][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-17 05:45:00.826][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-17 05:45:00.840][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-17 05:45:00.842][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-17 05:45:00.843][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-17 05:45:00.845][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-17 05:45:00.847][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-17 05:45:00.852][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-17 05:45:00.854][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-17 05:45:00.857][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-17 05:45:00.859][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-17 05:45:00.863][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-17 05:45:00.864][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-17 05:45:00.868][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-17 05:45:00.872][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-17 05:45:00.874][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-17 05:45:00.876][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-17 05:45:00.878][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-17 05:45:00.880][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-17 05:45:00.884][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-17 05:45:00.885][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-17 05:45:00.888][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:45:00.889][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:45:00.894][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-17 05:45:00.896][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-17 05:45:00.898][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-17 05:45:00.900][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-17 05:45:00.903][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-17 05:45:00.905][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-17 05:45:00.909][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-17 05:45:00.911][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-17 05:45:00.915][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-17 05:45:00.917][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-17 05:45:00.919][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-17 05:45:00.921][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-17 05:45:00.925][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-17 05:45:00.928][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-17 05:45:00.930][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-17 05:45:00.934][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-17 05:45:00.936][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-17 05:45:00.937][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-17 05:45:00.939][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.942][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:00.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:00.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:00.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:00.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:00.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:00.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:00.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:00.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:00.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:00.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:00.990][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[2023-10-17 05:45:00.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:00.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:00.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:00.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:00.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.001][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[2023-10-17 05:45:01.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.025][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[2023-10-17 05:45:01.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-17 05:45:01.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.128][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-10-17 05:45:01.130][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-10-17 05:45:01.133][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:01.134][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-10-17 05:45:01.135][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:01.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-17 05:45:01.141][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:01.142][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-17 05:45:01.143][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:01.145][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-10-17 05:45:01.146][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-10-17 05:45:01.148][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-17 05:45:01.149][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:01.150][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-10-17 05:45:01.152][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-10-17 05:45:01.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-10-17 05:45:01.155][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-17 05:45:01.157][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-17 05:45:01.157][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-17 05:45:01.157][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-17 05:45:01.158][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-17 05:45:01.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:01.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:01.165][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-17 05:45:01.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-17 05:45:01.168][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-17 05:45:01.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-17 05:45:01.171][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:45:01.171][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-10-17 05:45:01.175][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-17 05:45:01.177][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-17 05:45:01.178][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-17 05:45:01.180][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-10-17 05:45:01.180][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-10-17 05:45:01.182][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-17 05:45:01.184][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-17 05:45:01.186][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-10-17 05:45:01.190][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-17 05:45:01.192][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-17 05:45:01.194][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-17 05:45:01.199][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-10-17 05:45:01.201][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-10-17 05:45:01.203][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-10-17 05:45:01.205][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-10-17 05:45:01.206][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-17 05:45:01.208][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-17 05:45:01.211][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-10-17 05:45:01.213][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-10-17 05:45:01.214][biodb::testThat]
biodb.INFO [2023-10-17 05:45:01.217][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-10-17 05:45:01.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-17 05:45:01.221][biodb::testThat]
biodb.DEBUG[2023-10-17 05:45:01.226][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-10-17 05:45:01.232][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:45:01.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-10-17 05:45:01.236][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:45:01.238][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-10-17 05:45:01.245][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-10-17 05:45:01.250][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-10-17 05:45:01.253][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-10-17 05:45:01.254][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-10-17 05:45:01.257][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-10-17 05:45:01.264][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-10-17 05:45:01.265][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-10-17 05:45:01.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-10-17 05:45:01.271][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-10-17 05:45:01.273][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-10-17 05:45:01.275][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-10-17 05:45:01.276][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-10-17 05:45:01.278][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-10-17 05:45:01.279][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-10-17 05:45:01.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:01.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:01.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:01.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:01.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:01.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:01.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-17 05:45:01.300][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-10-17 05:45:01.303][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-10-17 05:45:01.304][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-10-17 05:45:01.306][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-10-17 05:45:02.193][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-10-17 05:45:03.042][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-10-17 05:45:03.045][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-10-17 05:45:03.052][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-10-17 05:45:03.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-10-17 05:45:03.062][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-10-17 05:45:03.064][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-10-17 05:45:03.068][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-10-17 05:45:03.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-17 05:45:03.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:03.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:03.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:03.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:03.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:03.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-17 05:45:03.109][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.111][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.115][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.126][ef$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:45:03.129][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:45:03.131][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.133][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.134][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-10-17 05:45:03.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-10-17 05:45:03.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.144][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:03.145][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:03.147][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.149][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-17 05:45:03.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-17 05:45:03.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.160][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-17 05:45:03.162][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-17 05:45:03.164][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.165][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.167][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-17 05:45:03.170][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-17 05:45:03.171][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.172][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.176][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:03.182][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:03.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.185][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.188][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:03.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-10-17 05:45:03.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.193][ef$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:45:03.195][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:45:03.196][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.198][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.202][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-10-17 05:45:03.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-17 05:45:03.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.208][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:03.209][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:03.211][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.212][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:03.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-10-17 05:45:03.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.224][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:03.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:03.227][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.228][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-17 05:45:03.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-17 05:45:03.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.238][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:45:03.239][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:45:03.240][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.242][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.243][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-10-17 05:45:03.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-10-17 05:45:03.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.254][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:45:03.255][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:45:03.256][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.258][ef$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.260][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-10-17 05:45:03.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-10-17 05:45:03.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:03.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:03.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:03.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:03.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-10-17 05:45:03.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-10-17 05:45:03.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-17 05:45:03.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-17 05:45:03.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-17 05:45:03.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-17 05:45:03.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-17 05:45:03.342][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-10-17 05:45:03.348][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-17 05:45:03.350][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-10-17 05:45:03.352][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-10-17 05:45:03.353][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-17 05:45:03.355][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-17 05:45:03.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-17 05:45:03.357][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-17 05:45:03.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-17 05:45:03.362][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-17 05:45:03.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
>
> proc.time()
user system elapsed
22.711 1.354 88.483
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.589 | 0.688 | 7.258 | |
| ChebiEntry | 0.417 | 0.019 | 0.616 | |