Back to Long Tests report for BioC 3.18

This page was generated on 2024-04-13 23:55:02 -0400 (Sat, 13 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4675
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4413
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4436
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 7/30HostnameOS / ArchCHECK
biodbExpasy 1.6.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-04-13 09:55:01 -0400 (Sat, 13 Apr 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_18
git_last_commit: abe7f92
git_last_commit_date: 2023-10-24 11:40:32 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbExpasy on palomino4


To the developers/maintainers of the biodbExpasy 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.

raw results

Summary

Package: biodbExpasy
Version: 1.6.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.6.0.tar.gz
StartedAt: 2024-04-13 16:04:28 -0400 (Sat, 13 Apr 2024)
EndedAt: 2024-04-13 16:05:18 -0400 (Sat, 13 Apr 2024)
EllapsedTime: 50.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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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.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-04-13 16:05:08.300][biodb::testContext]
biodb.INFO [2024-04-13 16:05:08.304][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:08.305][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-04-13 16:05:08.306][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:08.307][biodb::testContext]
biodb.INFO [2024-04-13 16:05:08.314][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:08.317][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:08.351][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:08.353][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:05:08.354][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:05:08.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.359][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:05:08.378][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:05:08.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.383][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:05:08.384][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:05:08.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.389][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:05:08.390][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:05:08.392][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:05:08.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.397][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:05:08.398][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:05:08.399][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:05:08.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.404][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:05:08.405][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:05:08.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.410][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:05:08.412][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:05:08.413][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:05:08.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.418][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:05:08.419][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:05:08.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.424][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:05:08.425][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:05:08.427][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:05:08.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.432][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:08.433][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:05:08.434][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:05:08.435][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:05:08.437][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:05:08.438][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:05:08.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.443][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:05:08.444][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:05:08.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.449][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:05:08.451][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:05:08.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.455][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:05:08.457][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:05:08.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.462][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:05:08.463][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:05:08.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.468][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:05:08.469][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:05:08.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.474][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:08.475][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:05:08.479][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:05:08.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.484][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:05:08.485][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:05:08.487][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:05:08.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.494][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:05:08.527][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.544][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-13 16:05:08.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.546][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:08.548][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.549][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.551][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.552][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.553][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:08.555][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:08.556][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.557][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:05:08.558][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:08.560][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.561][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.562][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:08.562][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:08.562][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:08.562][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:08.562][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:08.564][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:08.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:08.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:08.568][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:08.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:08.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:08.577][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.578][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.579][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:08.580][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:08.581][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.583][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.584][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:05:08.586][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.587][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:08.588][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.589][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:08.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.591][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.592][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.594][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.595][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:08.596][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:08.597][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.598][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:05:08.599][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:08.601][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.602][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.603][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:08.603][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:08.603][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:08.603][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:08.603][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:08.604][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:08.605][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:08.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:08.607][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:08.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:08.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:08.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.612][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:08.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:08.615][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.616][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.618][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:05:08.620][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.621][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-13 16:05:08.622][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.623][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:08.624][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.625][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.627][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.628][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.629][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:08.630][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:08.631][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.632][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:05:08.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:08.635][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.636][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.637][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.638][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:08.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:08.640][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:08.641][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:08.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:08.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:08.645][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.646][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.647][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:08.648][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:08.649][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.650][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.652][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:05:08.654][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.655][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:08.656][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.657][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:08.658][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.659][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.660][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.662][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.663][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:08.664][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:08.665][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.666][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:05:08.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:08.669][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.670][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:08.671][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.672][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:08.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:08.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:08.675][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:08.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:08.678][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:08.679][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:08.680][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.681][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:08.682][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:08.683][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:08.684][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:08.688][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:08.689][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.704][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[2024-04-13 16:05:08.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.767][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[2024-04-13 16:05:08.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.785][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:05:08.789][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:05:08.790][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:05:08.792][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:05:08.793][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:05:08.795][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:05:08.796][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:08.798][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:08.799][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:08.801][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:05:08.802][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:05:08.804][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:05:08.805][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:08.807][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:08.808][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:05:08.810][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:05:08.811][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:05:08.813][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:05:08.814][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:05:08.816][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:05:08.817][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:05:08.819][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:05:08.820][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:05:08.822][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:05:08.823][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:05:08.825][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:05:08.826][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:05:08.828][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:05:08.829][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:05:08.831][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:05:08.832][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:05:08.834][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:05:08.835][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:05:08.837][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:05:08.838][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:05:08.840][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:05:08.841][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:05:08.843][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:05:08.844][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:05:08.846][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:05:08.848][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:05:08.849][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:05:08.851][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:05:08.852][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:05:08.854][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:05:08.855][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:05:08.857][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:05:08.858][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:05:08.860][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:05:08.861][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:05:08.863][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:05:08.864][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:05:08.866][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:05:08.867][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:05:08.869][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:05:08.870][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:05:08.872][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:05:08.873][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:05:08.875][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:05:08.877][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:05:08.879][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:05:08.880][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:05:08.882][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:05:08.888][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:05:08.890][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:05:08.891][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:05:08.893][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:05:08.894][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:05:08.896][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:05:08.897][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:05:08.899][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:05:08.900][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:05:08.902][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:05:08.903][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:05:08.905][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:05:08.906][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:05:08.908][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:05:08.909][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:05:08.911][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:05:08.912][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:05:08.914][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:05:08.915][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:05:08.917][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:05:08.959][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:05:08.962][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:08.965][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:08.966][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.968][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:08.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:08.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:08.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:08.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:08.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:08.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:08.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:08.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:08.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:08.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:08.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:08.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:08.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:09.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:09.101][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:09.109][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:09.111][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:09.112][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-04-13 16:05:09.114][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:09.115][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:09.116][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:09.117][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:09.118][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:09.119][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:09.121][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-04-13 16:05:09.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:09.123][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:09.124][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-04-13 16:05:09.125][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:09.126][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-04-13 16:05:09.126][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:09.126][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:09.126][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:09.128][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:09.129][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:09.130][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:05:09.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:09.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:09.133][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:09.134][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:09.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:09.137][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:09.138][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:05:09.139][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:09.140][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:09.141][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:09.142][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:09.148][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:09.169][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:09.171][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-04-13 16:05:09.174][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:09.178][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-04-13 16:05:09.182][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:09.183][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:09.185][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-04-13 16:05:09.195][biodb::testThat]
biodb.INFO [2024-04-13 16:05:09.196][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-04-13 16:05:09.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:09.198][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:09.205][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-04-13 16:05:09.207][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:05:09.210][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:05:09.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:09.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:09.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.321][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.335][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.345][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:09.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.350][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.354][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.359][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.364][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:09.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.431][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.436][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.445][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:09.478][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-04-13 16:05:09.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:09.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:09.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.486][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:09.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:09.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:09.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:09.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.496][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:09.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:09.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.542][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.583][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.588][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.592][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.622][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.623][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.625][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.655][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.659][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.674][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.679][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.683][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.688][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.689][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.692][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.693][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.707][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.712][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.716][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.721][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.722][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.724][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.726][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.740][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.741][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.743][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.750][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.751][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.753][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.760][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.761][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.763][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.769][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.771][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.774][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.792][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-04-13 16:05:09.841][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:05:09.843][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:05:09.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:09.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:09.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:09.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:09.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:09.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:09.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:09.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.864][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:09.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:09.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:09.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.873][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:09.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:09.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.878][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.883][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.892][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:09.925][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-04-13 16:05:09.942][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:09.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:09.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:09.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:09.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.952][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:09.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:09.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.957][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:09.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:09.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.973][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:09.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:09.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:09.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:09.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:09.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.013][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:10.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:10.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.017][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:10.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:10.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.022][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:10.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:10.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.059][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.060][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.066][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:10.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:10.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:10.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:10.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:10.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:10.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.099][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:10.100][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:10.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.102][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:10.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:10.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.118][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.123][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.127][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.132][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.133][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.135][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.137][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.151][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:10.152][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:10.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.154][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.161][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.162][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:10.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.164][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:10.171][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:10.172][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:10.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:10.174][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:10.186][biodb::testThat]
biodb.INFO [2024-04-13 16:05:10.188][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-13 16:05:10.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:10.190][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:10.193][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-04-13 16:05:10.198][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-13 16:05:10.217][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-04-13 16:05:10.219][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-04-13 16:05:10.221][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-04-13 16:05:10.223][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-13 16:05:10.224][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-04-13 16:05:10.225][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:05:10.226][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-13 16:05:10.227][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-13 16:05:10.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:10.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:10.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:10.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:10.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:10.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:10.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:10.246][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-04-13 16:05:10.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-13 16:05:10.264][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-13 16:05:10.266][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-04-13 16:05:10.886][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-04-13 16:05:10.887][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-13 16:05:10.889][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-13 16:05:10.890][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-04-13 16:05:11.540][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-13 16:05:11.543][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-04-13 16:05:11.556][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-04-13 16:05:11.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:11.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:11.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:11.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:11.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:11.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:11.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:11.588][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-04-13 16:05:11.602][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-13 16:05:11.603][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-13 16:05:11.616][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-04-13 16:05:11.825][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2024-04-13 16:05:11.827][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-13 16:05:11.828][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-13 16:05:11.829][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-04-13 16:05:12.445][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-13 16:05:12.447][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-04-13 16:05:12.452][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-04-13 16:05:12.455][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-04-13 16:05:12.458][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-13 16:05:12.460][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-04-13 16:05:12.461][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:05:12.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:12.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:12.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:12.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:12.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:12.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:12.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:12.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.483][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:12.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:12.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.493][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:12.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:12.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.522][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.531][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.541][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:12.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:12.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:12.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:12.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:12.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:12.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:12.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:12.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.580][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:12.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:05:12.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:05:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:05:12.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.595][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.609][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:05:12.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:12.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:12.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:12.656][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-04-13 16:05:12.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:12.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:12.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:12.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:12.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:12.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:12.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:12.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:12.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:12.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:12.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:12.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:12.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:12.702][biodb::testThat]
biodb.INFO [2024-04-13 16:05:12.703][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-13 16:05:12.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:12.706][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:12.709][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.710][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.713][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:12.714][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-04-13 16:05:12.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:12.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:12.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:12.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:12.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:12.759][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:05:12.762][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:05:12.765][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-13 16:05:12.766][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-13 16:05:12.767][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-04-13 16:05:12.976][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2024-04-13 16:05:12.978][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-13 16:05:12.979][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-13 16:05:12.985][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-04-13 16:05:13.743][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-13 16:05:13.746][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-04-13 16:05:13.752][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-04-13 16:05:13.758][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-04-13 16:05:13.783][biodb::testThat]
biodb.INFO [2024-04-13 16:05:13.784][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-04-13 16:05:13.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:13.786][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:13.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:13.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:13.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:13.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:13.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:13.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:13.851][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:05:13.854][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-13 16:05:13.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-04-13 16:05:13.869][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-13 16:05:13.873][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-04-13 16:05:13.897][biodb::testThat]
biodb.INFO [2024-04-13 16:05:13.899][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-04-13 16:05:13.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:13.901][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:13.913][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:13.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:13.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:13.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:13.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:13.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:13.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:13.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:13.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.963][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:13.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:13.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:13.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:13.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.973][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:13.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:13.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:13.978][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:13.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:13.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:13.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:13.990][biodb::testThat]
biodb.INFO [2024-04-13 16:05:13.991][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-13 16:05:13.992][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:13.993][biodb::testThat]
biodb.INFO [2024-04-13 16:05:14.005][biodb::testThat]
biodb.INFO [2024-04-13 16:05:14.006][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-13 16:05:14.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:14.009][biodb::testThat]
biodb.INFO [2024-04-13 16:05:14.019][biodb::testThat]
biodb.INFO [2024-04-13 16:05:14.021][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-13 16:05:14.022][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:14.023][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:14.036][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-04-13 16:05:14.245][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-04-13 16:05:15.027][biodb::testThat]
biodb.INFO [2024-04-13 16:05:15.028][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-13 16:05:15.029][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:15.030][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:15.251][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-04-13 16:05:17.169][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:17.171][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:17.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:17.173][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:17.174][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:17.176][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:17.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:17.178][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:17.179][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:05:17.181][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-04-13 16:05:17.182][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-04-13 16:05:17.183][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:05:17.184][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.186][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.188][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-13 16:05:17.199][biodb::testContext]
biodb.INFO [2024-04-13 16:05:17.200][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:17.201][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-04-13 16:05:17.202][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:17.203][biodb::testContext]
biodb.INFO [2024-04-13 16:05:17.206][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:17.208][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:17.213][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:17.214][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:05:17.216][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:05:17.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.220][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:05:17.235][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:05:17.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.239][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:05:17.240][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:05:17.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.245][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:05:17.246][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:05:17.247][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:05:17.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.252][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:05:17.253][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:05:17.254][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:05:17.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.258][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:05:17.260][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:05:17.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.264][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:05:17.265][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:05:17.266][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:05:17.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.271][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:05:17.272][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:05:17.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.276][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:05:17.277][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:05:17.279][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:05:17.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.282][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[2024-04-13 16:05:17.283][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:17.284][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:05:17.285][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:05:17.287][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:05:17.288][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:05:17.294][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:05:17.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.299][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:05:17.300][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:05:17.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.304][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:05:17.305][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:05:17.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.310][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:05:17.311][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:05:17.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.315][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:05:17.316][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:05:17.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.321][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:05:17.322][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:05:17.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.326][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:17.328][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:05:17.331][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:05:17.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.336][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:05:17.337][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:05:17.338][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:05:17.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.343][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:05:17.345][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.346][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-13 16:05:17.347][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.348][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:17.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.352][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.358][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.359][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:17.360][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:17.361][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.363][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:05:17.364][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:17.365][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.366][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.368][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:17.368][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:17.368][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:17.368][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:17.368][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:17.369][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:17.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.372][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:17.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.377][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:17.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:17.380][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.381][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.383][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:05:17.385][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.386][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:17.387][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.388][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:17.389][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.391][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.392][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.393][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.394][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:17.395][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:17.397][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.398][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:05:17.399][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:17.400][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.401][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.403][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:17.403][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:17.403][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:17.403][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:17.403][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:17.404][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:17.405][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.407][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:17.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.412][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.413][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:17.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:17.415][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.416][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.418][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:05:17.420][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.421][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-13 16:05:17.422][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:17.424][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.427][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.428][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.429][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:17.430][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:17.432][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.433][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:05:17.434][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:17.435][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.436][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.437][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.439][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:17.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.441][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.442][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:17.443][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.445][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.447][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.448][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:17.449][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:17.450][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.451][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.453][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:05:17.454][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.456][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:17.457][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.458][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:17.459][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.460][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.463][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.464][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:17.465][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:17.466][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.468][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:05:17.469][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:17.470][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.471][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.472][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.474][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:17.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.477][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:17.478][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.479][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.480][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.481][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.483][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:17.484][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:17.485][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.486][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.488][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:17.489][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.559][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[2024-04-13 16:05:17.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.588][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:05:17.590][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:05:17.591][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:05:17.593][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:05:17.594][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:05:17.596][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:05:17.597][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:17.599][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:17.600][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:17.602][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:05:17.603][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:05:17.605][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:05:17.607][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:17.608][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:17.610][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:05:17.611][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:05:17.613][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:05:17.614][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:05:17.616][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:05:17.617][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:05:17.619][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:05:17.620][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:05:17.622][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:05:17.623][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:05:17.625][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:05:17.626][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:05:17.628][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:05:17.629][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:05:17.631][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:05:17.633][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:05:17.634][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:05:17.636][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:05:17.637][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:05:17.639][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:05:17.640][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:05:17.642][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:05:17.643][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:05:17.645][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:05:17.646][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:05:17.648][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:05:17.649][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:05:17.651][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:05:17.652][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:05:17.654][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:05:17.655][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:05:17.657][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:05:17.659][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:05:17.660][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:05:17.662][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:05:17.663][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:05:17.665][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:05:17.666][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:05:17.668][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:05:17.669][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:05:17.671][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:05:17.672][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:05:17.674][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:05:17.675][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:05:17.677][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:05:17.678][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:05:17.680][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:05:17.681][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:05:17.683][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:05:17.685][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:05:17.686][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:05:17.688][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:05:17.689][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:05:17.691][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:05:17.692][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:05:17.694][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:05:17.695][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:05:17.697][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:05:17.698][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:05:17.700][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:05:17.702][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:05:17.703][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:05:17.705][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:05:17.706][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:05:17.708][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:05:17.709][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:05:17.711][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:05:17.712][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:05:17.714][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:05:17.715][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:05:17.718][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:17.719][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:17.720][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.722][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.805][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.DEBUG[2024-04-13 16:05:17.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:17.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:17.861][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:17.862][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:17.864][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.865][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-04-13 16:05:17.867][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.868][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:17.869][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.870][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.871][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.873][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.874][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-04-13 16:05:17.875][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:17.876][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.877][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-04-13 16:05:17.879][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:17.880][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-04-13 16:05:17.880][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:17.880][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:17.880][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:05:17.881][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:17.882][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:17.883][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:05:17.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.886][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.887][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:17.888][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:17.889][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:17.890][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:17.891][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:05:17.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:17.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:17.895][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:17.896][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:17.897][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:17.901][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:17.902][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-04-13 16:05:17.903][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:05:17.905][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-04-13 16:05:17.907][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:17.908][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:17.909][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-04-13 16:05:17.910][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:05:17.911][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-04-13 16:05:17.913][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-04-13 16:05:17.914][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:05:17.915][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:17.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:17.917][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:17.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:17.919][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:17.920][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
   4.93    0.62   11.57

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbExpasy/DESCRIPTION' ... OK
* this is package 'biodbExpasy' 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 whether package 'biodbExpasy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log'
for details.

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package 'biodbExpasy' ...
** 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 (biodbExpasy)