Back to Long Tests report for BioC 3.20

This page was generated on 2024-11-16 23:55 -0500 (Sat, 16 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4765
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
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 7/32HostnameOS / ArchCHECK
biodbExpasy 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-11-16 09:55 -0500 (Sat, 16 Nov 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_20
git_last_commit: 4403c2f
git_last_commit_date: 2024-10-29 11:09:35 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on lconway

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: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
StartedAt: 2024-11-16 16:01:07 -0500 (Sat, 16 Nov 2024)
EndedAt: 2024-11-16 16:05:41 -0500 (Sat, 16 Nov 2024)
EllapsedTime: 274.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-11-16 16:05:34.239][biodb::testContext]
biodb.INFO [2024-11-16 16:05:34.242][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-16 16:05:34.243][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-11-16 16:05:34.244][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-16 16:05:34.245][biodb::testContext]
biodb.INFO [2024-11-16 16:05:34.251][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-16 16:05:34.252][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-16 16:05:34.259][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:05:34.260][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-16 16:05:34.261][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-16 16:05:34.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.264][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-16 16:05:34.290][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-16 16:05:34.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.293][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-16 16:05:34.294][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-16 16:05:34.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.297][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-16 16:05:34.298][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-16 16:05:34.299][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-16 16:05:34.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.301][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-16 16:05:34.302][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-16 16:05:34.303][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-16 16:05:34.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.306][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-16 16:05:34.306][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-16 16:05:34.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.309][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-16 16:05:34.310][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-16 16:05:34.311][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-16 16:05:34.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.314][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-16 16:05:34.314][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-16 16:05:34.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.317][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-16 16:05:34.318][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-16 16:05:34.319][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-16 16:05:34.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.321][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-16 16:05:34.322][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-16 16:05:34.323][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-16 16:05:34.324][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-16 16:05:34.324][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-16 16:05:34.325][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-16 16:05:34.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.328][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-16 16:05:34.329][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-16 16:05:34.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.332][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-16 16:05:34.333][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-16 16:05:34.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.336][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-16 16:05:34.337][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-16 16:05:34.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.340][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-16 16:05:34.341][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-16 16:05:34.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.344][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-16 16:05:34.345][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-16 16:05:34.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.348][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-16 16:05:34.349][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-16 16:05:34.367][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-16 16:05:34.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.371][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-16 16:05:34.372][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-16 16:05:34.373][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-16 16:05:34.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.378][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-16 16:05:34.404][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.416][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-16 16:05:34.417][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.418][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:34.419][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.420][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.421][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.421][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.422][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-16 16:05:34.423][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:34.424][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.424][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-16 16:05:34.425][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:34.426][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.427][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.428][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:05:34.428][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-16 16:05:34.428][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-16 16:05:34.428][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-16 16:05:34.428][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-16 16:05:34.428][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:05:34.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.431][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:34.432][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.434][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:34.435][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:34.436][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.437][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.438][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-16 16:05:34.439][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.440][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-16 16:05:34.441][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.441][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:34.442][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.443][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.443][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.444][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.445][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-16 16:05:34.446][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:34.446][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.447][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-16 16:05:34.448][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:34.449][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.449][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.450][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:05:34.450][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-16 16:05:34.450][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-16 16:05:34.450][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-16 16:05:34.450][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-16 16:05:34.451][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:05:34.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.453][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:34.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.460][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.461][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.461][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:34.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:34.463][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.463][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.464][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-16 16:05:34.465][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.466][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-16 16:05:34.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.468][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:34.468][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.469][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.470][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.470][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.471][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-16 16:05:34.472][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:34.473][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.473][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-16 16:05:34.474][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:34.475][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.475][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.476][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.477][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:05:34.478][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.479][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:34.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.481][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.482][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.482][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:34.483][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:34.484][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.484][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.485][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-16 16:05:34.487][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.487][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-16 16:05:34.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:34.490][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.490][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.491][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.492][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.492][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-16 16:05:34.493][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:34.494][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.495][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-16 16:05:34.495][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:34.496][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.497][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.498][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.498][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:05:34.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:34.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.504][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:34.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:34.506][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.507][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.509][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:05:34.510][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.538][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[2024-11-16 16:05:34.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.568][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-16 16:05:34.571][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-16 16:05:34.572][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-16 16:05:34.573][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-16 16:05:34.574][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-16 16:05:34.575][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-16 16:05:34.576][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-16 16:05:34.577][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-16 16:05:34.578][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-16 16:05:34.579][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-16 16:05:34.580][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-16 16:05:34.581][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-16 16:05:34.582][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-16 16:05:34.583][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-16 16:05:34.584][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-16 16:05:34.584][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-16 16:05:34.585][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-16 16:05:34.586][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-16 16:05:34.587][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-16 16:05:34.588][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-16 16:05:34.589][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-16 16:05:34.591][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-16 16:05:34.592][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-16 16:05:34.593][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-16 16:05:34.594][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-16 16:05:34.595][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-16 16:05:34.596][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-16 16:05:34.601][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-16 16:05:34.602][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-16 16:05:34.603][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-16 16:05:34.604][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-16 16:05:34.605][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-16 16:05:34.606][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-16 16:05:34.608][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-16 16:05:34.609][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-16 16:05:34.610][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-16 16:05:34.611][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-16 16:05:34.612][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-16 16:05:34.613][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-16 16:05:34.614][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-16 16:05:34.615][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-16 16:05:34.616][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-16 16:05:34.617][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-16 16:05:34.618][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-16 16:05:34.619][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-16 16:05:34.620][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-16 16:05:34.621][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-16 16:05:34.622][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-16 16:05:34.623][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-16 16:05:34.624][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-16 16:05:34.625][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-16 16:05:34.626][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-16 16:05:34.627][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-16 16:05:34.628][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-16 16:05:34.629][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-16 16:05:34.630][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-16 16:05:34.631][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-16 16:05:34.632][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-16 16:05:34.633][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-16 16:05:34.634][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-16 16:05:34.635][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-16 16:05:34.636][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-16 16:05:34.637][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-16 16:05:34.638][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-16 16:05:34.639][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-16 16:05:34.640][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-16 16:05:34.641][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-16 16:05:34.642][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-16 16:05:34.643][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-16 16:05:34.644][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-16 16:05:34.645][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-16 16:05:34.646][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-16 16:05:34.647][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-16 16:05:34.648][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-16 16:05:34.649][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-16 16:05:34.651][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-16 16:05:34.652][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-16 16:05:34.653][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-16 16:05:34.654][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-16 16:05:34.655][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-16 16:05:34.656][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-16 16:05:34.657][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-16 16:05:34.658][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-16 16:05:34.662][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-16 16:05:34.664][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-16 16:05:34.666][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:05:34.667][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.668][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.699][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[2024-11-16 16:05:34.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.704][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[2024-11-16 16:05:34.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.730][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[2024-11-16 16:05:34.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:34.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:34.754][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-11-16 16:05:34.761][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-11-16 16:05:34.762][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.763][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-11-16 16:05:34.764][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.765][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:34.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.767][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.768][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-11-16 16:05:34.769][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:34.770][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.771][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-11-16 16:05:34.771][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:34.772][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-11-16 16:05:34.772][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-11-16 16:05:34.772][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-11-16 16:05:34.772][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-11-16 16:05:34.773][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:34.773][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:05:34.774][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-16 16:05:34.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.776][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:34.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:34.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:34.778][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:34.779][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-11-16 16:05:34.780][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:34.780][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:34.781][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:34.782][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:34.786][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-16 16:05:34.804][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-11-16 16:05:34.805][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-11-16 16:05:34.808][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-11-16 16:05:34.811][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-11-16 16:05:34.815][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-16 16:05:34.815][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-16 16:05:34.816][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-11-16 16:05:34.824][biodb::testThat]
biodb.INFO [2024-11-16 16:05:34.825][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-11-16 16:05:34.825][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:34.826][biodb::testThat]
biodb.TRACE[2024-11-16 16:05:34.829][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-11-16 16:05:34.830][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-11-16 16:05:34.833][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-11-16 16:05:34.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:05:34.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:34.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:34.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:34.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:34.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:34.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-16 16:05:34.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:34.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:34.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.883][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:34.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:34.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.904][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:34.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:34.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.910][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-11-16 16:05:34.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.914][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.917][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.919][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.922][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-11-16 16:05:34.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:34.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:34.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:34.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:34.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:34.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:34.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:34.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:34.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:34.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:34.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.977][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:34.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:34.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.980][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:34.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:34.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:34.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:34.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.987][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:34.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:34.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:34.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:34.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:34.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:34.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:34.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:34.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:34.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:34.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:05:35.035][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-11-16 16:05:35.037][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:05:35.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:05:35.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:05:35.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:05:35.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.043][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-16 16:05:35.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-16 16:05:35.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.046][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-16 16:05:35.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-16 16:05:35.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.075][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.103][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.106][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.109][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.128][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.130][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.151][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.152][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.153][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.169][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.172][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.175][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.179][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.179][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.181][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.181][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.191][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.194][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.198][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.200][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.201][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.203][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.203][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.213][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.214][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.216][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.220][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.221][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.222][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.227][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.227][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.229][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.233][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.234][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.235][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.249][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-11-16 16:05:35.278][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-11-16 16:05:35.279][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-11-16 16:05:35.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:05:35.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:35.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:35.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:35.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:35.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:35.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-16 16:05:35.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.293][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.299][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-11-16 16:05:35.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:35.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.303][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.306][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.312][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:05:35.334][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-11-16 16:05:35.349][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:05:35.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:05:35.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.352][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:05:35.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:05:35.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.355][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-16 16:05:35.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-16 16:05:35.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-16 16:05:35.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-16 16:05:35.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.368][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.400][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.403][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.406][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:35.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.433][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.434][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.436][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.456][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.457][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.459][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.470][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.473][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.476][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.480][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.480][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.482][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.483][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.493][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:35.493][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:35.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.495][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.499][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.500][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:35.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.502][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:35.506][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:35.507][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:35.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:35.509][ef$get] fields variable is a list.
biodb.INFO [2024-11-16 16:05:35.516][biodb::testThat]
biodb.INFO [2024-11-16 16:05:35.517][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-16 16:05:35.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:35.518][biodb::testThat]
biodb.DEBUG[2024-11-16 16:05:35.520][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-11-16 16:05:35.526][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-11-16 16:05:35.529][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-11-16 16:05:35.535][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-11-16 16:05:35.536][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-11-16 16:05:35.537][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-16 16:05:35.537][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-11-16 16:05:35.538][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-11-16 16:05:35.539][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-16 16:05:35.540][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-16 16:05:35.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:05:35.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:35.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:35.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:35.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:35.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:35.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:35.553][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-11-16 16:05:35.569][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-16 16:05:35.570][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-16 16:05:35.571][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-11-16 16:05:36.521][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-11-16 16:05:36.885][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-16 16:05:36.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-11-16 16:05:36.899][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-11-16 16:05:36.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:05:36.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:36.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:36.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:36.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:36.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:36.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:36.925][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-11-16 16:05:36.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-16 16:05:36.937][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-16 16:05:36.948][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-11-16 16:05:37.467][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-11-16 16:05:37.826][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-16 16:05:37.836][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-11-16 16:05:37.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-11-16 16:05:37.841][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-11-16 16:05:37.842][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-16 16:05:37.843][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-11-16 16:05:37.844][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-11-16 16:05:37.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:05:37.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:37.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:37.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:37.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:37.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:37.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-16 16:05:37.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.858][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:37.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:37.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:37.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:37.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.865][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-11-16 16:05:37.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:37.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:37.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:37.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:37.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:37.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:37.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:37.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:37.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:37.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:37.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:37.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.883][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.886][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.892][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:05:37.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:05:37.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:37.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:37.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:37.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:37.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:37.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-16 16:05:37.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.917][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:37.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-11-16 16:05:37.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:37.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:37.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.924][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-11-16 16:05:37.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-11-16 16:05:37.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.927][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.933][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.939][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-11-16 16:05:37.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:05:37.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:05:37.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:05:37.968][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-11-16 16:05:37.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-16 16:05:37.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-16 16:05:37.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-16 16:05:37.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-16 16:05:37.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-16 16:05:37.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-16 16:05:37.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-16 16:05:37.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-16 16:05:37.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-16 16:05:37.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-16 16:05:37.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:37.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-16 16:05:37.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-16 16:05:37.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:37.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-16 16:05:37.998][biodb::testThat]
biodb.INFO [2024-11-16 16:05:37.999][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-16 16:05:37.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:38.000][biodb::testThat]
biodb.TRACE[2024-11-16 16:05:38.002][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:38.003][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:38.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.005][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:05:38.006][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-11-16 16:05:38.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:38.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:38.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:38.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:38.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:38.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:38.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:05:38.042][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-11-16 16:05:38.043][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-11-16 16:05:38.045][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-16 16:05:38.046][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-16 16:05:38.047][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-11-16 16:05:38.438][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-11-16 16:05:38.830][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-16 16:05:38.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-11-16 16:05:38.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-11-16 16:05:38.840][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-11-16 16:05:38.855][biodb::testThat]
biodb.INFO [2024-11-16 16:05:38.856][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-11-16 16:05:38.857][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:38.858][biodb::testThat]
biodb.TRACE[2024-11-16 16:05:38.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:38.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:38.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:38.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:38.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:38.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:38.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:38.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:38.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:05:38.939][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-11-16 16:05:38.941][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-16 16:05:38.952][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-11-16 16:05:38.953][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-16 16:05:38.954][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-11-16 16:05:38.970][biodb::testThat]
biodb.INFO [2024-11-16 16:05:38.971][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-11-16 16:05:38.972][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:38.972][biodb::testThat]
biodb.TRACE[2024-11-16 16:05:38.981][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:05:38.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:05:38.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:38.984][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:05:38.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:05:38.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:38.987][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-16 16:05:38.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-16 16:05:38.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:38.991][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-16 16:05:38.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-16 16:05:38.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:38.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:39.022][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:05:39.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:05:39.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:39.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:39.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:05:39.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:05:39.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:39.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:39.028][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-16 16:05:39.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-16 16:05:39.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:39.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:39.031][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-16 16:05:39.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-16 16:05:39.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:39.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-16 16:05:39.039][biodb::testThat]
biodb.INFO [2024-11-16 16:05:39.040][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-16 16:05:39.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:39.041][biodb::testThat]
biodb.INFO [2024-11-16 16:05:39.049][biodb::testThat]
biodb.INFO [2024-11-16 16:05:39.050][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-16 16:05:39.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:39.051][biodb::testThat]
biodb.INFO [2024-11-16 16:05:39.058][biodb::testThat]
biodb.INFO [2024-11-16 16:05:39.059][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-16 16:05:39.060][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:39.061][biodb::testThat]
biodb.DEBUG[2024-11-16 16:05:39.071][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[2024-11-16 16:05:39.452][getUrlContent] Use RCurl 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 [2024-11-16 16:05:39.844][biodb::testThat]
biodb.INFO [2024-11-16 16:05:39.845][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-16 16:05:39.846][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:05:39.847][biodb::testThat]
biodb.DEBUG[2024-11-16 16:05:40.223][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-11-16 16:05:40.605][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:40.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:40.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:40.608][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:05:40.609][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:05:40.610][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:05:40.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:05:40.611][ef$get] fields variable is a list.
biodb.INFO [2024-11-16 16:05:40.612][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-16 16:05:40.613][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-11-16 16:05:40.614][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-11-16 16:05:40.615][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-16 16:05:40.615][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:40.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:40.617][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.618][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-16 16:05:40.635][biodb::testContext]
biodb.INFO [2024-11-16 16:05:40.635][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-16 16:05:40.636][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-11-16 16:05:40.637][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-16 16:05:40.638][biodb::testContext]
biodb.INFO [2024-11-16 16:05:40.639][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-16 16:05:40.640][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-16 16:05:40.643][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:05:40.644][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-16 16:05:40.645][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-16 16:05:40.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.648][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-16 16:05:40.648][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-16 16:05:40.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.651][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-16 16:05:40.652][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-16 16:05:40.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.655][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-16 16:05:40.656][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-16 16:05:40.656][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-16 16:05:40.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.659][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-16 16:05:40.660][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-16 16:05:40.661][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-16 16:05:40.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.664][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-16 16:05:40.665][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-16 16:05:40.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.667][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-16 16:05:40.668][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-16 16:05:40.669][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-16 16:05:40.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.672][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-16 16:05:40.673][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-16 16:05:40.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.675][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-16 16:05:40.676][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-16 16:05:40.677][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-16 16:05:40.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.680][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-16 16:05:40.680][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-16 16:05:40.681][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-16 16:05:40.682][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-16 16:05:40.683][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-16 16:05:40.684][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-16 16:05:40.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.686][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-16 16:05:40.687][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-16 16:05:40.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.690][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-16 16:05:40.691][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-16 16:05:40.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.693][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-16 16:05:40.694][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-16 16:05:40.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.697][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-16 16:05:40.698][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-16 16:05:40.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.700][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-16 16:05:40.701][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-16 16:05:40.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.704][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-16 16:05:40.705][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-16 16:05:40.720][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-16 16:05:40.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.723][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-16 16:05:40.724][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-16 16:05:40.725][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-16 16:05:40.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.731][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[2024-11-16 16:05:40.732][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-16 16:05:40.733][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.734][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-16 16:05:40.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.736][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:40.736][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.737][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.738][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.738][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.739][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-16 16:05:40.740][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:40.741][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.741][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-16 16:05:40.742][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:40.743][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.743][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.744][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:05:40.744][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-16 16:05:40.744][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-16 16:05:40.744][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-16 16:05:40.744][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-16 16:05:40.745][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:05:40.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:40.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:40.747][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:40.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:40.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:40.749][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.750][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.751][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:40.752][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:40.753][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.753][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.754][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-16 16:05:40.755][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.756][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-16 16:05:40.757][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.758][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:40.759][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.760][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.760][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.761][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.762][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-16 16:05:40.762][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:40.763][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.764][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-16 16:05:40.765][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:40.766][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.766][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.767][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:05:40.767][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-16 16:05:40.767][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-16 16:05:40.767][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-16 16:05:40.767][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-16 16:05:40.768][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:05:40.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:40.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:40.770][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:40.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:40.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:40.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.773][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.774][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:40.775][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:40.776][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.776][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.777][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-16 16:05:40.778][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.779][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-16 16:05:40.780][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.781][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:40.782][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.783][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.784][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.784][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-16 16:05:40.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:40.786][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.787][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-16 16:05:40.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:40.788][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.789][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.790][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.790][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:05:40.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:40.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:40.793][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:40.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:40.794][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:40.795][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.796][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.796][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:40.797][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:40.798][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.799][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.799][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-16 16:05:40.801][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.801][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-16 16:05:40.802][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.803][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:40.804][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.804][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.805][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.806][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.806][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-16 16:05:40.807][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:40.808][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.809][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-16 16:05:40.809][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:40.810][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.811][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:40.812][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.813][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:05:40.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:40.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:40.819][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:40.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:40.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:40.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:40.822][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.822][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:40.823][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:40.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:40.825][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:40.826][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:05:40.826][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.886][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-16 16:05:40.887][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-16 16:05:40.888][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-16 16:05:40.889][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-16 16:05:40.890][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-16 16:05:40.891][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-16 16:05:40.892][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-16 16:05:40.894][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-16 16:05:40.895][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-16 16:05:40.896][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-16 16:05:40.897][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-16 16:05:40.898][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-16 16:05:40.899][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-16 16:05:40.904][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-16 16:05:40.906][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-16 16:05:40.907][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-16 16:05:40.908][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-16 16:05:40.909][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-16 16:05:40.910][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-16 16:05:40.911][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-16 16:05:40.912][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-16 16:05:40.913][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-16 16:05:40.915][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-16 16:05:40.915][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-16 16:05:40.916][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-16 16:05:40.917][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-16 16:05:40.918][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-16 16:05:40.919][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-16 16:05:40.920][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-16 16:05:40.921][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-16 16:05:40.923][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-16 16:05:40.924][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-16 16:05:40.925][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-16 16:05:40.926][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-16 16:05:40.927][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-16 16:05:40.928][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-16 16:05:40.929][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-16 16:05:40.930][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-16 16:05:40.931][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-16 16:05:40.933][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-16 16:05:40.934][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-16 16:05:40.935][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-16 16:05:40.936][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-16 16:05:40.937][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-16 16:05:40.938][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-16 16:05:40.939][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-16 16:05:40.940][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-16 16:05:40.941][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-16 16:05:40.942][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-16 16:05:40.943][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-16 16:05:40.944][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-16 16:05:40.945][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-16 16:05:40.946][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-16 16:05:40.948][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-16 16:05:40.949][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-16 16:05:40.950][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-16 16:05:40.951][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-16 16:05:40.952][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-16 16:05:40.953][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-16 16:05:40.954][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-16 16:05:40.955][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-16 16:05:40.956][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-16 16:05:40.957][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-16 16:05:40.958][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-16 16:05:40.959][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-16 16:05:40.960][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-16 16:05:40.961][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-16 16:05:40.962][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-16 16:05:40.963][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-16 16:05:40.964][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-16 16:05:40.965][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-16 16:05:40.966][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-16 16:05:40.967][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-16 16:05:40.968][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-16 16:05:40.970][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-16 16:05:40.971][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-16 16:05:40.972][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-16 16:05:40.973][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-16 16:05:40.974][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-16 16:05:40.975][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-16 16:05:40.976][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-16 16:05:40.977][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-16 16:05:40.978][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-16 16:05:40.979][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-16 16:05:40.980][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-16 16:05:40.981][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:05:40.982][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.983][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:40.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:40.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:40.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:40.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:40.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:40.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:40.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:40.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:40.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.017][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[2024-11-16 16:05:41.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:05:41.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:05:41.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.068][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[2024-11-16 16:05:41.070][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-11-16 16:05:41.075][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-11-16 16:05:41.077][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:41.077][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-11-16 16:05:41.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:41.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:05:41.079][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:41.080][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:05:41.081][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:41.082][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:05:41.082][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-11-16 16:05:41.083][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:05:41.084][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:41.085][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-11-16 16:05:41.085][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:05:41.086][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-11-16 16:05:41.086][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-11-16 16:05:41.086][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-11-16 16:05:41.086][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-11-16 16:05:41.087][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-16 16:05:41.087][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:05:41.088][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-16 16:05:41.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:41.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:41.090][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:05:41.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:05:41.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:05:41.092][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:05:41.093][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-11-16 16:05:41.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:05:41.094][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:05:41.095][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-16 16:05:41.096][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:05:41.097][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-16 16:05:41.100][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-11-16 16:05:41.100][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-11-16 16:05:41.101][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-11-16 16:05:41.102][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-11-16 16:05:41.103][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-16 16:05:41.104][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-16 16:05:41.105][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-11-16 16:05:41.105][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-16 16:05:41.106][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-11-16 16:05:41.107][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-11-16 16:05:41.108][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-16 16:05:41.108][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:05:41.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:05:41.110][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:05:41.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:05:41.111][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:05:41.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using 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 ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... 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’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-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
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)