Back to Long Tests report for BioC 3.20

This page was generated on 2024-07-06 23:55 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
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 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-06 09:55 -0400 (Sat, 06 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino6Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  


CHECK results for biodbExpasy on nebbiolo2

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: 1.9.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-07-06 16:01:51 -0400 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 16:02:34 -0400 (Sat, 06 Jul 2024)
EllapsedTime: 43.0 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-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-07-06 16:02:27.729][biodb::testContext]
biodb.INFO [2024-07-06 16:02:27.732][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:02:27.733][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-06 16:02:27.734][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:02:27.735][biodb::testContext]
biodb.INFO [2024-07-06 16:02:27.742][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:02:27.744][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:02:27.752][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:02:27.753][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:02:27.754][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:02:27.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.758][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:02:27.778][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:02:27.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.781][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:02:27.782][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:02:27.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.786][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:02:27.787][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:02:27.788][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:02:27.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.792][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:02:27.793][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:02:27.794][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:02:27.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.798][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:02:27.799][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:02:27.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.802][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:02:27.803][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:02:27.804][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:02:27.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.808][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:02:27.809][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:02:27.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.813][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:02:27.814][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:02:27.815][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:02:27.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.818][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:02:27.819][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:02:27.820][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:02:27.821][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:02:27.822][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:02:27.824][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:02:27.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.827][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:02:27.828][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:02:27.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.832][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:02:27.833][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:02:27.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.837][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:02:27.838][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:02:27.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.841][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:02:27.842][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:02:27.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.846][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:02:27.847][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:02:27.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.851][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:02:27.852][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:02:27.856][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:02:27.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.860][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:02:27.861][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:02:27.862][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:02:27.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:27.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:27.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:27.869][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:02:27.905][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:27.929][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-06 16:02:27.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:27.931][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.932][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:27.933][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:27.934][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:27.935][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:02:27.936][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:27.937][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.938][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:02:27.939][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:27.939][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:27.940][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.941][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:02:27.941][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:02:27.941][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:02:27.941][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:02:27.941][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:02:27.942][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:02:27.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:27.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:27.945][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:27.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:27.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:27.947][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:27.948][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:27.949][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:27.949][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:27.950][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:27.951][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:27.952][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:02:27.954][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:27.955][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:02:27.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.957][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:27.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:27.959][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:27.960][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:27.961][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:02:27.962][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:27.963][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.964][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:02:27.965][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:27.966][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:27.966][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.967][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:02:27.967][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:02:27.967][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:02:27.967][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:02:27.967][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:02:27.968][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:02:27.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:27.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:27.971][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:27.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:27.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:27.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:27.974][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:27.975][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:27.976][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:27.977][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:27.978][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:27.979][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:02:27.980][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.981][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-06 16:02:27.982][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.983][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:27.984][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.985][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:27.986][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:27.986][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:27.987][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:02:27.988][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:27.989][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:27.990][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:02:27.991][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:27.992][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:27.993][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:27.994][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:27.994][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:02:27.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:27.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:27.997][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:27.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:27.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:27.999][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:28.000][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:28.001][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:28.002][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:28.003][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:28.004][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:28.005][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:02:28.006][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.007][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:02:28.008][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.009][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:28.010][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.011][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:28.011][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:28.012][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:28.013][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:02:28.014][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:28.015][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:28.016][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:02:28.017][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:28.018][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:28.018][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.019][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:28.020][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:02:28.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:28.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:28.023][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:28.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:28.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:28.025][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:28.026][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:28.027][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:28.028][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:28.028][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:28.029][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:28.033][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:02:28.034][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.035][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[2024-07-06 16:02:28.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.113][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:02:28.119][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:02:28.120][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:02:28.122][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:02:28.123][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:02:28.125][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:02:28.126][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:02:28.127][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:02:28.129][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:02:28.130][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:02:28.131][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:02:28.133][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:02:28.134][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:02:28.135][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:02:28.137][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:02:28.138][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:02:28.139][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:02:28.141][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:02:28.142][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:02:28.144][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:02:28.145][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:02:28.146][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:02:28.148][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:02:28.149][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:02:28.150][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:02:28.152][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:02:28.153][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:02:28.154][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:02:28.156][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:02:28.157][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:02:28.158][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:02:28.160][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:02:28.161][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:02:28.162][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:02:28.164][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:02:28.165][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:02:28.167][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:02:28.168][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:02:28.182][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:02:28.183][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:02:28.185][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:02:28.186][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:02:28.187][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:02:28.189][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:02:28.190][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:02:28.191][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:02:28.193][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:02:28.194][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:02:28.195][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:02:28.197][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:02:28.198][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:02:28.200][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:02:28.201][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:02:28.202][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:02:28.204][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:02:28.205][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:02:28.207][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:02:28.208][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:02:28.209][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:02:28.211][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:02:28.212][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:02:28.214][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:02:28.215][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:02:28.216][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:02:28.218][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:02:28.219][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:02:28.220][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:02:28.222][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:02:28.223][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:02:28.224][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:02:28.226][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:02:28.227][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:02:28.228][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:02:28.230][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:02:28.231][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:02:28.232][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:02:28.234][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:02:28.235][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:02:28.236][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:02:28.238][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:02:28.239][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:02:28.240][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:02:28.242][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:02:28.248][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:02:28.249][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:02:28.253][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:02:28.254][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.255][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.296][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[2024-07-06 16:02:28.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.313][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[2024-07-06 16:02:28.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.335][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[2024-07-06 16:02:28.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:28.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:28.359][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-07-06 16:02:28.367][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:02:28.369][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:28.370][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-07-06 16:02:28.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.372][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:28.373][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:28.374][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.375][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:28.376][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-07-06 16:02:28.377][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:28.378][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.379][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-07-06 16:02:28.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:28.381][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-07-06 16:02:28.381][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:02:28.381][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:02:28.381][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:02:28.382][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:28.382][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:02:28.383][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:02:28.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:28.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:28.386][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:28.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:28.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:28.388][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:28.389][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-07-06 16:02:28.390][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:28.391][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:28.392][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:28.392][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:28.398][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:02:28.420][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:02:28.426][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-07-06 16:02:28.430][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:02:28.434][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-07-06 16:02:28.438][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:02:28.439][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:02:28.440][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-07-06 16:02:28.449][biodb::testThat]
biodb.INFO [2024-07-06 16:02:28.450][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-06 16:02:28.450][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:28.451][biodb::testThat]
biodb.TRACE[2024-07-06 16:02:28.455][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-07-06 16:02:28.456][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:02:28.460][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-06 16:02:28.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:02:28.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:02:28.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.521][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.535][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.542][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:02:28.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.546][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.550][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.553][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.557][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:02:28.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.623][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.627][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.634][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:02:28.666][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-07-06 16:02:28.668][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:02:28.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:02:28.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.672][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:02:28.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:02:28.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.675][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:02:28.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:02:28.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:02:28.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:02:28.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.710][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.740][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.744][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.747][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.767][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.768][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.770][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.791][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.792][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.794][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.805][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.808][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.812][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.815][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.816][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.818][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.819][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.828][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.832][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.835][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.839][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.840][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.842][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.842][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.874][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.875][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.877][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.881][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.882][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.883][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.887][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.888][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.890][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.893][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.896][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.911][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-07-06 16:02:28.943][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:02:28.944][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-06 16:02:28.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:02:28.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:28.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:28.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:28.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:28.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:28.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:02:28.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.960][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:28.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:28.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:28.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.967][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:02:28.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:28.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.971][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.975][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.982][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:28.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:02:29.007][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-07-06 16:02:29.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:02:29.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:02:29.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:02:29.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:02:29.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:02:29.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:02:29.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.036][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:02:29.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:02:29.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.047][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.080][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.084][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.087][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.116][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.117][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.119][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.140][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.141][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.143][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.153][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.157][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.160][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.164][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.165][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.166][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.167][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.177][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.178][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.180][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.183][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.184][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.186][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.189][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.190][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.192][ef$get] fields variable is a list.
biodb.INFO [2024-07-06 16:02:29.198][biodb::testThat]
biodb.INFO [2024-07-06 16:02:29.199][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-06 16:02:29.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:29.201][biodb::testThat]
biodb.DEBUG[2024-07-06 16:02:29.202][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-07-06 16:02:29.209][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-06 16:02:29.214][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.TRACE[2024-07-06 16:02:29.215][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-06 16:02:29.216][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt".
biodb.DEBUG[2024-07-06 16:02:29.217][conn$getEntryContent] 2 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-07-06 16:02:29.219][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-07-06 16:02:29.220][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-06 16:02:29.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:02:29.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:29.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:29.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:29.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:29.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:29.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:02:29.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.235][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.242][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:02:29.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:29.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.268][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.272][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.279][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:02:29.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:02:29.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:29.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:29.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:29.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:29.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:29.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:02:29.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-06 16:02:29.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.314][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-06 16:02:29.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-06 16:02:29.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.322][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.329][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-06 16:02:29.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:02:29.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:02:29.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:02:29.364][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-07-06 16:02:29.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:02:29.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:02:29.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:02:29.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:02:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:02:29.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:02:29.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:02:29.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:02:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:02:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:02:29.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:02:29.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:02:29.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:02:29.395][biodb::testThat]
biodb.INFO [2024-07-06 16:02:29.396][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-06 16:02:29.397][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:29.398][biodb::testThat]
biodb.TRACE[2024-07-06 16:02:29.400][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.401][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.403][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:02:29.404][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-07-06 16:02:29.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:29.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:29.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:29.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:29.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:02:29.439][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-07-06 16:02:29.443][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-07-06 16:02:29.466][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-06 16:02:29.467][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-06 16:02:29.468][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-07-06 16:02:30.309][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-07-06 16:02:30.755][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-06 16:02:30.758][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-07-06 16:02:30.771][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-07-06 16:02:30.777][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-07-06 16:02:30.790][biodb::testThat]
biodb.INFO [2024-07-06 16:02:30.791][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-06 16:02:30.792][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:30.793][biodb::testThat]
biodb.TRACE[2024-07-06 16:02:30.815][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:30.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:30.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:30.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:30.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:30.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:30.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:02:30.879][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-07-06 16:02:30.882][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-06 16:02:30.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-07-06 16:02:30.897][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-06 16:02:30.898][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-07-06 16:02:30.912][biodb::testThat]
biodb.INFO [2024-07-06 16:02:30.913][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-06 16:02:30.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:30.915][biodb::testThat]
biodb.TRACE[2024-07-06 16:02:30.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:02:30.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:02:30.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.926][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:02:30.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:02:30.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.930][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:02:30.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:02:30.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.933][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:02:30.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:02:30.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.966][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:02:30.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:02:30.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.970][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:02:30.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:02:30.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:02:30.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:02:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:30.977][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:02:30.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:02:30.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:30.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:02:30.985][biodb::testThat]
biodb.INFO [2024-07-06 16:02:30.985][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-06 16:02:30.986][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:30.987][biodb::testThat]
biodb.INFO [2024-07-06 16:02:31.000][biodb::testThat]
biodb.INFO [2024-07-06 16:02:31.000][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-06 16:02:31.001][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:31.002][biodb::testThat]
biodb.INFO [2024-07-06 16:02:31.009][biodb::testThat]
biodb.INFO [2024-07-06 16:02:31.010][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-06 16:02:31.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:31.011][biodb::testThat]
biodb.DEBUG[2024-07-06 16:02:31.024][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[2024-07-06 16:02:31.456][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 [2024-07-06 16:02:32.071][biodb::testThat]
biodb.INFO [2024-07-06 16:02:32.073][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-06 16:02:32.074][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:02:32.075][biodb::testThat]
biodb.DEBUG[2024-07-06 16:02:32.513][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-07-06 16:02:33.100][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:33.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:33.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:33.103][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:02:33.104][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:02:33.105][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:02:33.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:02:33.107][ef$get] fields variable is a list.
biodb.INFO [2024-07-06 16:02:33.108][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:02:33.110][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-07-06 16:02:33.111][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-07-06 16:02:33.112][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:02:33.113][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.114][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.116][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-06 16:02:33.128][biodb::testContext]
biodb.INFO [2024-07-06 16:02:33.129][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:02:33.130][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-07-06 16:02:33.131][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:02:33.132][biodb::testContext]
biodb.INFO [2024-07-06 16:02:33.134][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:02:33.135][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:02:33.139][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:02:33.140][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:02:33.141][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:02:33.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.145][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:02:33.146][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:02:33.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.149][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:02:33.150][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:02:33.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.154][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:02:33.155][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:02:33.156][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:02:33.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.159][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:02:33.160][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:02:33.161][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:02:33.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.165][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:02:33.166][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:02:33.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.169][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:02:33.170][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:02:33.171][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:02:33.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.175][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:02:33.176][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:02:33.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.179][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:02:33.180][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:02:33.181][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:02:33.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.185][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:02:33.186][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:02:33.187][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:02:33.188][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:02:33.189][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:02:33.190][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:02:33.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.193][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:02:33.194][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:02:33.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.198][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:02:33.199][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:02:33.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.202][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:02:33.203][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:02:33.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.207][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:02:33.208][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:02:33.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.227][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:02:33.228][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:02:33.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.231][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:02:33.232][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:02:33.235][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:02:33.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.239][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:02:33.240][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:02:33.241][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:02:33.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.245][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:02:33.247][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.248][self$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[2024-07-06 16:02:33.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.250][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:33.251][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.252][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.253][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.254][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.254][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:02:33.255][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:33.256][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.257][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:02:33.258][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:33.259][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.260][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.261][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:02:33.261][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:02:33.261][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:02:33.261][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:02:33.261][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:02:33.262][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:02:33.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.265][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:33.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.267][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.268][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:33.270][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:33.271][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.272][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.273][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:02:33.274][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.275][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:02:33.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.277][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:33.278][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.279][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.280][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.281][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.282][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:02:33.282][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:33.283][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.284][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:02:33.285][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:33.286][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.287][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.288][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:02:33.288][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:02:33.288][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:02:33.288][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:02:33.288][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:02:33.289][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:02:33.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.291][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:33.292][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.294][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.295][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:33.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:33.297][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.298][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.299][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:02:33.301][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.301][self$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[2024-07-06 16:02:33.302][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.303][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:33.304][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.305][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.306][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.307][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.308][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:02:33.308][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:33.309][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.310][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:02:33.311][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:33.312][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.313][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.314][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.315][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:02:33.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.317][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:33.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.321][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.321][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:33.322][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:33.323][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.324][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.325][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:02:33.326][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.327][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:02:33.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.329][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:33.330][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.331][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.332][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.333][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.333][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:02:33.334][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:33.335][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.336][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:02:33.337][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:33.338][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.339][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.340][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.341][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:02:33.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.343][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:33.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.345][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.346][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.347][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:33.348][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:33.349][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.350][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.351][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:02:33.352][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.425][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:02:33.426][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:02:33.427][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:02:33.428][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:02:33.430][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:02:33.431][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:02:33.432][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:02:33.433][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:02:33.435][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:02:33.436][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:02:33.437][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:02:33.438][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:02:33.440][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:02:33.441][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:02:33.442][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:02:33.443][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:02:33.445][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:02:33.446][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:02:33.447][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:02:33.448][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:02:33.450][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:02:33.451][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:02:33.452][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:02:33.453][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:02:33.455][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:02:33.456][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:02:33.457][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:02:33.458][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:02:33.460][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:02:33.461][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:02:33.462][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:02:33.463][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:02:33.465][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:02:33.466][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:02:33.467][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:02:33.468][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:02:33.469][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:02:33.471][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:02:33.472][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:02:33.473][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:02:33.474][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:02:33.476][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:02:33.477][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:02:33.478][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:02:33.479][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:02:33.481][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:02:33.482][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:02:33.483][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:02:33.484][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:02:33.486][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:02:33.487][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:02:33.488][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:02:33.489][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:02:33.491][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:02:33.492][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:02:33.493][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:02:33.494][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:02:33.496][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:02:33.497][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:02:33.498][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:02:33.499][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:02:33.501][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:02:33.502][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:02:33.503][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:02:33.504][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:02:33.505][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:02:33.507][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:02:33.508][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:02:33.509][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:02:33.510][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:02:33.512][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:02:33.513][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:02:33.514][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:02:33.515][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:02:33.517][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:02:33.518][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:02:33.519][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:02:33.520][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:02:33.522][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:02:33.523][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:02:33.524][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:02:33.525][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:02:33.527][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:02:33.528][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:02:33.529][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:02:33.530][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:02:33.531][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.533][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.544][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[2024-07-06 16:02:33.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.554][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[2024-07-06 16:02:33.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.560][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[2024-07-06 16:02:33.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:02:33.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:02:33.633][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-07-06 16:02:33.634][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:02:33.636][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.637][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-07-06 16:02:33.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:02:33.640][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.641][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.641][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.642][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.643][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-07-06 16:02:33.644][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:02:33.645][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.646][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-07-06 16:02:33.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:02:33.648][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-07-06 16:02:33.648][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:02:33.648][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:02:33.648][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-07-06 16:02:33.649][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:02:33.649][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:02:33.650][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:02:33.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.653][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:02:33.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:02:33.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:02:33.655][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:02:33.656][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-07-06 16:02:33.657][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:02:33.658][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:02:33.659][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:02:33.660][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:02:33.661][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:02:33.664][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:02:33.665][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-07-06 16:02:33.666][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-07-06 16:02:33.667][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-07-06 16:02:33.668][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:02:33.669][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:02:33.670][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-07-06 16:02:33.671][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:02:33.672][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-07-06 16:02:33.673][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-07-06 16:02:33.674][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:02:33.674][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:02:33.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:02:33.676][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:02:33.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:02:33.678][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:02:33.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 83 ]

══ 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 83 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* 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 ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... 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 83 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)