Long Tests report for BioC 3.22 - CHECK results for biodbNcbi on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4887
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4677
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CHECK results for biodbNcbi on lconway

To the developers/maintainers of the biodbNcbi 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: biodbNcbi

Version: 1.13.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.13.1.tar.gz

StartedAt: 2025-10-18 16:01:15 -0400 (Sat, 18 Oct 2025)

EndedAt: 2025-10-18 16:02:12 -0400 (Sat, 18 Oct 2025)

EllapsedTime: 56.9 seconds

RetCode: 1

Status: ERROR

CheckDir: biodbNcbi.Rcheck

Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2025-10-18 16:02:04.792][biodb::testContext]
biodb.INFO [2025-10-18 16:02:04.795][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:04.796][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-10-18 16:02:04.796][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:04.797][biodb::testContext]
biodb.INFO [2025-10-18 16:02:04.802][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:04.804][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:04.809][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:04.810][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-18 16:02:04.811][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-18 16:02:04.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.814][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-18 16:02:04.828][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-18 16:02:04.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.840][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-18 16:02:04.841][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-18 16:02:04.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.844][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-18 16:02:04.845][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-18 16:02:04.846][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-18 16:02:04.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.848][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-18 16:02:04.849][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-18 16:02:04.850][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-18 16:02:04.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.853][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-18 16:02:04.853][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-18 16:02:04.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.856][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-18 16:02:04.857][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-18 16:02:04.857][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-18 16:02:04.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.860][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-18 16:02:04.861][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-18 16:02:04.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.863][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-18 16:02:04.864][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-18 16:02:04.865][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-18 16:02:04.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.868][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:04.868][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-18 16:02:04.869][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-18 16:02:04.870][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-18 16:02:04.871][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-18 16:02:04.871][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-18 16:02:04.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.874][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-18 16:02:04.875][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-18 16:02:04.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.877][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-18 16:02:04.878][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-18 16:02:04.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.881][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-18 16:02:04.881][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-18 16:02:04.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.884][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-18 16:02:04.885][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-18 16:02:04.886][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-18 16:02:04.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.888][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:04.889][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-18 16:02:04.906][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-18 16:02:04.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.909][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-18 16:02:04.910][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-18 16:02:04.911][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-18 16:02:04.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:04.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:04.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:04.915][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-18 16:02:04.938][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:04.950][self$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[2025-10-18 16:02:04.952][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:04.953][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.954][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:04.955][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:04.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:04.956][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:04.957][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:04.958][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.958][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-18 16:02:04.959][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:04.960][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:04.961][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.961][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:04.961][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:04.961][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:04.961][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:04.961][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:04.962][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:04.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:04.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:04.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:04.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:04.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:04.966][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:04.967][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:04.968][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:04.968][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:04.969][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:04.970][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:04.971][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-18 16:02:04.976][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:04.977][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:04.978][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.978][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:04.979][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:04.980][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:04.981][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:04.982][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:04.983][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:04.983][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.984][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-18 16:02:04.985][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:04.986][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:04.986][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.987][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:04.987][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:04.987][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:04.987][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:04.987][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:04.988][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:04.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:04.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:04.990][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:04.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:04.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:04.992][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:04.993][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:04.994][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:04.995][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:04.995][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:04.996][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:04.997][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-18 16:02:04.998][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:04.999][self$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[2025-10-18 16:02:05.000][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.000][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:05.001][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.002][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.003][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.004][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.004][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:05.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:05.006][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.007][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-18 16:02:05.007][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:05.008][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.009][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.010][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.010][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:05.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:05.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.015][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:05.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:05.017][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.018][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.019][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-18 16:02:05.021][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.021][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:05.022][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.023][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:05.024][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.027][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:05.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:05.028][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.029][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-18 16:02:05.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:05.031][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.032][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.032][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.033][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:05.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:05.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.038][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.039][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:05.040][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:05.041][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.042][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.044][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:05.045][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.056][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[2025-10-18 16:02:05.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.069][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[2025-10-18 16:02:05.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.082][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[2025-10-18 16:02:05.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.086][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[2025-10-18 16:02:05.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.103][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[2025-10-18 16:02:05.104][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-18 16:02:05.107][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-18 16:02:05.108][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-18 16:02:05.109][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-18 16:02:05.110][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-18 16:02:05.111][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-18 16:02:05.112][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:05.113][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:05.114][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-18 16:02:05.115][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-18 16:02:05.116][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-18 16:02:05.117][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-18 16:02:05.118][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:05.119][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:05.120][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:05.121][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:05.122][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-18 16:02:05.123][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-18 16:02:05.124][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-18 16:02:05.125][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-18 16:02:05.127][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-18 16:02:05.128][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-18 16:02:05.129][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-18 16:02:05.130][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-18 16:02:05.131][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-18 16:02:05.132][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-18 16:02:05.133][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-18 16:02:05.134][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-18 16:02:05.135][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-18 16:02:05.136][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-18 16:02:05.137][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-18 16:02:05.139][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-18 16:02:05.140][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-18 16:02:05.141][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-18 16:02:05.142][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-18 16:02:05.143][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-18 16:02:05.144][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-18 16:02:05.145][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-18 16:02:05.146][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-18 16:02:05.147][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-18 16:02:05.149][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-18 16:02:05.150][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-18 16:02:05.151][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-18 16:02:05.152][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-18 16:02:05.153][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-18 16:02:05.154][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:05.155][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-18 16:02:05.156][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-18 16:02:05.157][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-18 16:02:05.158][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-18 16:02:05.160][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-18 16:02:05.161][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-18 16:02:05.162][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-18 16:02:05.163][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-18 16:02:05.164][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-18 16:02:05.165][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-18 16:02:05.166][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-18 16:02:05.167][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-18 16:02:05.168][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-18 16:02:05.169][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-18 16:02:05.170][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-18 16:02:05.171][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-18 16:02:05.172][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-18 16:02:05.173][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-18 16:02:05.174][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-18 16:02:05.175][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-18 16:02:05.176][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-18 16:02:05.178][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-18 16:02:05.179][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-18 16:02:05.180][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-18 16:02:05.181][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-18 16:02:05.182][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-18 16:02:05.183][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-18 16:02:05.184][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-18 16:02:05.185][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-18 16:02:05.186][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-18 16:02:05.187][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-18 16:02:05.188][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-18 16:02:05.189][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-18 16:02:05.190][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-18 16:02:05.191][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-18 16:02:05.192][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-18 16:02:05.193][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-18 16:02:05.198][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-18 16:02:05.199][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:05.202][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:05.203][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.204][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.256][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[2025-10-18 16:02:05.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.266][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[2025-10-18 16:02:05.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.284][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[2025-10-18 16:02:05.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:05.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:05.290][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:05.298][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-18 16:02:05.299][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.300][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-18 16:02:05.300][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.301][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:05.302][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.303][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.304][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.305][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-18 16:02:05.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:05.306][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.307][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-18 16:02:05.308][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:05.308][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-18 16:02:05.308][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-18 16:02:05.309][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.310][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.311][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:05.312][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.313][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:05.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.316][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-18 16:02:05.316][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-18 16:02:05.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:05.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:05.318][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.319][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.320][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-18 16:02:05.321][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.322][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-18 16:02:05.322][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.323][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:05.324][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.325][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.325][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.326][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.327][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:05.328][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:05.328][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.329][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-18 16:02:05.330][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:05.331][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-18 16:02:05.331][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-18 16:02:05.331][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-18 16:02:05.331][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-18 16:02:05.331][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-18 16:02:05.331][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-18 16:02:05.331][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.332][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:05.333][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:05.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.335][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:05.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.338][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.339][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:05.339][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:05.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:05.340][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:05.341][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.341][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.342][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-18 16:02:05.344][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.345][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-18 16:02:05.349][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.350][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:05.351][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.351][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.352][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.353][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.354][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:05.354][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:05.355][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.356][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.357][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:05.358][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.359][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:05.359][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:05.359][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:05.360][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-18 16:02:05.361][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.362][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:05.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.364][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.365][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.365][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:05.365][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:05.365][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-18 16:02:05.366][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:05.367][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:05.368][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.369][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-18 16:02:05.370][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-18 16:02:05.371][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.372][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-18 16:02:05.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:05.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.376][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.378][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:05.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:05.379][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.380][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-18 16:02:05.381][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:05.382][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-18 16:02:05.382][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-18 16:02:05.383][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:05.384][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:05.385][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-18 16:02:05.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.387][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:05.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:05.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:05.389][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:05.390][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:05.390][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:05.390][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-18 16:02:05.390][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:05.391][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:05.392][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:05.393][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-18 16:02:05.398][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-18 16:02:05.399][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:05.400][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:05.401][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-18 16:02:05.402][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:05.403][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-18 16:02:05.421][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-10-18 16:02:05.432][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-10-18 16:02:05.440][biodb::testThat]
biodb.INFO [2025-10-18 16:02:05.441][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-18 16:02:05.442][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:05.442][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:05.446][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-10-18 16:02:05.447][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:02:05.449][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-10-18 16:02:05.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:02:05.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-18 16:02:05.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.497][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:05.516][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.518][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.538][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:05.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.542][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.551][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:05.639][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-10-18 16:02:05.642][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.645][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.666][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:05.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:05.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:05.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:05.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:05.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:05.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.676][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:05.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:05.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.694][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.724][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.728][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.736][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.755][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.756][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.757][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.768][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:05.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.775][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.778][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:05.778][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.780][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.781][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:05.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.791][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.792][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.794][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.798][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.799][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.801][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.815][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-10-18 16:02:05.847][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:02:05.848][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-10-18 16:02:05.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:02:05.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:05.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:05.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:05.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:05.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:05.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-18 16:02:05.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.884][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:05.885][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.887][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.888][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.895][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.901][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:05.922][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-10-18 16:02:05.943][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.947][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:05.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.950][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:05.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:05.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.953][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:05.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:05.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.957][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:05.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:05.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.960][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:05.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:05.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:05.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:05.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:05.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:05.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:05.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:06.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:06.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.002][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:06.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:06.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.006][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:06.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:06.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.009][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:06.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:06.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:06.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:06.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:06.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:06.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:06.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:06.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.042][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:06.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:06.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.045][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:06.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:06.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.057][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:06.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.060][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.063][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.066][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:06.067][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.069][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.070][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-18 16:02:06.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.081][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.082][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:06.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.083][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:06.088][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:06.089][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:06.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:06.091][ef$get] fields variable is a list.
biodb.INFO [2025-10-18 16:02:06.098][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.099][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-18 16:02:06.100][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:06.101][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:06.103][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-10-18 16:02:06.107][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-10-18 16:02:06.109][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-18 16:02:06.110][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:06.111][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-18 16:02:06.112][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:06.113][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:06.147][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.148][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-18 16:02:06.149][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:06.150][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.156][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.157][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-18 16:02:06.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:06.164][biodb::testThat]
biodb.WARN [2025-10-18 16:02:06.180][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-18 16:02:06.199][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-18 16:02:06.210][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.211][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-18 16:02:06.212][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:06.212][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:06.226][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-10-18 16:02:06.267][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:06.291][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-18 16:02:06.292][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:06.293][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-18 16:02:06.294][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:06.294][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:06.324][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.325][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-18 16:02:06.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:06.327][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.343][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.344][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-18 16:02:06.345][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:06.346][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.353][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.354][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:06.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:06.356][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.368][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.369][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:06.370][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:06.370][biodb::testThat]
biodb.INFO [2025-10-18 16:02:06.376][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-18 16:02:06.377][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-10-18 16:02:06.377][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-18 16:02:06.378][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.380][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.381][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-18 16:02:06.389][biodb::testContext]
biodb.INFO [2025-10-18 16:02:06.390][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:06.390][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-10-18 16:02:06.391][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:06.392][biodb::testContext]
biodb.INFO [2025-10-18 16:02:06.393][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:06.395][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:06.398][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:06.399][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-18 16:02:06.400][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-18 16:02:06.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.403][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-18 16:02:06.403][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-18 16:02:06.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.406][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-18 16:02:06.407][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-18 16:02:06.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.410][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-18 16:02:06.411][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-18 16:02:06.411][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-18 16:02:06.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.414][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-18 16:02:06.415][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-18 16:02:06.416][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-18 16:02:06.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.419][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-18 16:02:06.420][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-18 16:02:06.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.422][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-18 16:02:06.423][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-18 16:02:06.424][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-18 16:02:06.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.427][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-18 16:02:06.428][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-18 16:02:06.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.430][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-18 16:02:06.431][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-18 16:02:06.436][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-18 16:02:06.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.439][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:06.440][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-18 16:02:06.440][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-18 16:02:06.441][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-18 16:02:06.442][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-18 16:02:06.443][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-18 16:02:06.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.445][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-18 16:02:06.446][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-18 16:02:06.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.449][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-18 16:02:06.450][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-18 16:02:06.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.452][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-18 16:02:06.453][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-18 16:02:06.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.456][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-18 16:02:06.456][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-18 16:02:06.457][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-18 16:02:06.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.460][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:06.461][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-18 16:02:06.478][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-18 16:02:06.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.481][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-18 16:02:06.482][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-18 16:02:06.483][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-18 16:02:06.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.485][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-18 16:02:06.487][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.487][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-18 16:02:06.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:06.490][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.490][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.491][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.492][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.493][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:06.494][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:06.494][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.495][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-18 16:02:06.496][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:06.497][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.497][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.498][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:06.498][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:06.498][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:06.498][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:06.498][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:06.499][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:06.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.502][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:06.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.504][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.505][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.506][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:06.506][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:06.507][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.508][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.509][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-18 16:02:06.510][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.511][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:06.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:06.513][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.514][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.515][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.515][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.516][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:06.517][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:06.518][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.519][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-18 16:02:06.519][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:06.520][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.521][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.522][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:06.522][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:06.522][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:06.522][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:06.522][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:06.522][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:06.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.524][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.525][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:06.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.527][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.527][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.528][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.529][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:06.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:06.530][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.531][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.532][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-18 16:02:06.534][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.534][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-18 16:02:06.535][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.536][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:06.536][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.537][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.538][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.539][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.543][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:06.544][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:06.545][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.545][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-18 16:02:06.546][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:06.547][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.548][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.548][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.549][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:06.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.551][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:06.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.554][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.555][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:06.556][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:06.557][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.558][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.559][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-18 16:02:06.560][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.561][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:06.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.562][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:06.563][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.564][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.567][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:06.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:06.568][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.569][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-18 16:02:06.570][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:06.571][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.572][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.573][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.574][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:06.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.575][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.576][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:06.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.579][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.579][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.580][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:06.581][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:06.581][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.582][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.583][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:06.584][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.588][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[2025-10-18 16:02:06.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.604][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[2025-10-18 16:02:06.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.621][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[2025-10-18 16:02:06.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.643][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-18 16:02:06.644][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-18 16:02:06.646][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-18 16:02:06.647][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-18 16:02:06.648][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-18 16:02:06.649][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-18 16:02:06.650][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:06.651][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:06.652][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-18 16:02:06.653][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-18 16:02:06.654][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-18 16:02:06.655][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-18 16:02:06.656][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:06.657][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:06.658][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:06.659][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:06.660][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-18 16:02:06.661][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-18 16:02:06.662][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-18 16:02:06.664][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-18 16:02:06.665][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-18 16:02:06.666][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-18 16:02:06.667][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-18 16:02:06.668][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-18 16:02:06.669][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-18 16:02:06.670][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-18 16:02:06.671][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-18 16:02:06.672][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-18 16:02:06.673][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-18 16:02:06.674][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-18 16:02:06.675][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-18 16:02:06.676][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-18 16:02:06.677][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-18 16:02:06.678][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-18 16:02:06.679][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-18 16:02:06.680][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-18 16:02:06.681][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-18 16:02:06.682][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-18 16:02:06.683][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-18 16:02:06.684][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-18 16:02:06.685][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-18 16:02:06.686][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-18 16:02:06.687][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-18 16:02:06.688][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-18 16:02:06.689][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-18 16:02:06.690][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:06.691][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-18 16:02:06.692][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-18 16:02:06.693][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-18 16:02:06.694][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-18 16:02:06.695][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-18 16:02:06.696][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-18 16:02:06.697][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-18 16:02:06.698][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-18 16:02:06.699][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-18 16:02:06.700][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-18 16:02:06.701][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-18 16:02:06.702][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-18 16:02:06.703][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-18 16:02:06.704][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-18 16:02:06.705][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-18 16:02:06.706][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-18 16:02:06.707][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-18 16:02:06.708][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-18 16:02:06.709][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-18 16:02:06.710][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-18 16:02:06.711][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-18 16:02:06.712][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-18 16:02:06.714][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-18 16:02:06.715][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-18 16:02:06.716][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-18 16:02:06.721][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-18 16:02:06.722][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-18 16:02:06.723][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-18 16:02:06.724][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-18 16:02:06.725][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-18 16:02:06.726][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-18 16:02:06.727][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-18 16:02:06.729][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-18 16:02:06.730][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-18 16:02:06.731][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-18 16:02:06.732][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-18 16:02:06.733][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-18 16:02:06.734][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-18 16:02:06.735][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:06.736][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:06.736][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.738][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.780][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[2025-10-18 16:02:06.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.812][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[2025-10-18 16:02:06.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.817][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[2025-10-18 16:02:06.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:06.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:06.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:06.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:06.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:06.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:06.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:06.825][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:06.833][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-18 16:02:06.835][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.836][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-18 16:02:06.837][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.837][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:06.838][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.839][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.840][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.841][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.842][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-18 16:02:06.842][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:06.844][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.845][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-18 16:02:06.845][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:06.846][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-18 16:02:06.846][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-18 16:02:06.847][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.848][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.849][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:06.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.851][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:06.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.854][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.855][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-18 16:02:06.855][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-18 16:02:06.856][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:06.856][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:06.857][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.858][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.859][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-18 16:02:06.861][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.862][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-18 16:02:06.862][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.863][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:06.864][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.866][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.866][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.868][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.869][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:06.870][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:06.871][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.872][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-18 16:02:06.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:06.875][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-18 16:02:06.875][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-18 16:02:06.875][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-18 16:02:06.875][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-18 16:02:06.875][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-18 16:02:06.875][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-18 16:02:06.877][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.878][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:06.879][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:06.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:06.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.888][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:06.888][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:06.889][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:06.890][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:06.892][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.893][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.895][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-18 16:02:06.898][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.899][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-18 16:02:06.901][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.902][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:06.903][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.905][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.906][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.907][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.908][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:06.909][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:06.910][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.911][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-18 16:02:06.912][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.913][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:06.915][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.916][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:06.916][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:06.916][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:06.918][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-18 16:02:06.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:06.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.930][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.930][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:06.930][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:06.930][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-18 16:02:06.931][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:06.932][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:06.933][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.934][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-18 16:02:06.935][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-18 16:02:06.936][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.937][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-18 16:02:06.938][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.939][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:06.940][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.941][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.942][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.943][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.944][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:06.946][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:06.947][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.948][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-18 16:02:06.950][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:06.951][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-18 16:02:06.951][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-18 16:02:06.952][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:06.953][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:06.954][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-18 16:02:06.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.956][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:06.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:06.957][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:06.958][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:06.959][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:06.959][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:06.959][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-18 16:02:06.960][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:06.961][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:06.962][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:06.962][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-18 16:02:06.963][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-18 16:02:06.965][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:06.966][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:06.967][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-18 16:02:06.969][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:06.970][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-18 16:02:06.976][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-10-18 16:02:07.047][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-10-18 16:02:07.051][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.052][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-18 16:02:07.052][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.053][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:07.058][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-10-18 16:02:07.059][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:02:07.061][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-10-18 16:02:07.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:02:07.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-18 16:02:07.080][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.081][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.083][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.096][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:07.097][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:07.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.099][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.100][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:07.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:07.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.104][ef$get] Asked field names are: location.
biodb.TRACE[2025-10-18 16:02:07.104][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-10-18 16:02:07.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.106][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.107][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-10-18 16:02:07.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-10-18 16:02:07.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.115][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-10-18 16:02:07.116][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-10-18 16:02:07.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.117][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.118][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-10-18 16:02:07.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-10-18 16:02:07.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.122][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-10-18 16:02:07.122][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:07.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.124][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.125][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-10-18 16:02:07.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:07.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.128][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-10-18 16:02:07.129][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-10-18 16:02:07.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.131][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.133][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-10-18 16:02:07.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-10-18 16:02:07.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.139][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:07.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:07.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-18 16:02:07.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-18 16:02:07.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.146][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-18 16:02:07.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-18 16:02:07.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.153][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-18 16:02:07.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-18 16:02:07.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:07.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:07.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:07.175][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-10-18 16:02:07.177][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:07.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:07.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.180][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:07.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:07.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.183][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:07.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:07.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.187][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:07.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:07.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:07.190][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:07.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:07.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:07.193][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-10-18 16:02:07.218][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-10-18 16:02:07.229][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-10-18 16:02:07.230][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-10-18 16:02:07.233][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:07.234][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-18 16:02:07.235][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:07.236][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-18 16:02:07.237][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:07.238][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:07.249][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.249][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-18 16:02:07.250][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.251][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:07.253][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-10-18 16:02:07.253][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-10-18 16:02:07.254][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-18 16:02:07.255][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:07.256][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:07.257][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:07.258][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:07.259][private$retrieveContents] Get entry content(s) for 8 id(s)...
biodb.INFO [2025-10-18 16:02:07.285][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.286][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-18 16:02:07.287][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.288][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:07.290][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:07.291][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:07.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:07.292][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:07.294][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-10-18 16:02:07.302][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-18 16:02:07.303][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:07.304][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-18 16:02:07.305][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:07.306][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:07.307][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:07.307][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:07.321][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:07.350][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.350][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-18 16:02:07.351][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.352][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:07.359][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-18 16:02:07.359][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:07.361][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-18 16:02:07.361][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:07.362][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:07.363][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:07.364][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:07.364][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:07.378][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.378][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-18 16:02:07.379][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.380][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:07.383][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-18 16:02:07.384][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:07.385][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-18 16:02:07.386][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:07.387][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:07.388][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:07.388][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:07.389][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:07.403][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.404][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-18 16:02:07.405][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.406][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.417][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.418][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-18 16:02:07.419][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.419][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.426][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.427][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:07.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.428][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.444][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.445][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:07.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:07.446][biodb::testThat]
biodb.INFO [2025-10-18 16:02:07.452][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-18 16:02:07.453][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-10-18 16:02:07.454][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-10-18 16:02:07.454][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-18 16:02:07.455][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.456][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.458][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-18 16:02:07.462][biodb::testContext]
biodb.INFO [2025-10-18 16:02:07.462][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:07.463][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-10-18 16:02:07.464][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:07.465][biodb::testContext]
biodb.INFO [2025-10-18 16:02:07.466][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:07.468][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:07.471][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:07.472][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-18 16:02:07.473][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-18 16:02:07.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.476][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-18 16:02:07.477][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-18 16:02:07.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.480][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-18 16:02:07.481][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-18 16:02:07.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.484][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-18 16:02:07.484][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-18 16:02:07.485][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-18 16:02:07.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.488][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-18 16:02:07.489][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-18 16:02:07.490][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-18 16:02:07.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.493][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-18 16:02:07.493][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-18 16:02:07.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.496][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-18 16:02:07.497][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-18 16:02:07.498][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-18 16:02:07.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.501][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-18 16:02:07.502][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-18 16:02:07.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.505][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-18 16:02:07.506][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-18 16:02:07.507][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-18 16:02:07.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.510][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:07.511][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-18 16:02:07.511][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-18 16:02:07.512][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-18 16:02:07.513][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-18 16:02:07.514][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-18 16:02:07.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.517][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-18 16:02:07.518][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-18 16:02:07.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.526][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-18 16:02:07.526][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-18 16:02:07.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.529][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-18 16:02:07.530][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-18 16:02:07.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.533][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[2025-10-18 16:02:07.533][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-18 16:02:07.534][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-18 16:02:07.535][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-18 16:02:07.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.538][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:07.539][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-18 16:02:07.568][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-18 16:02:07.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.571][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-18 16:02:07.572][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-18 16:02:07.573][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-18 16:02:07.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.577][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-18 16:02:07.578][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.580][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-18 16:02:07.581][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.582][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:07.583][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.584][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.585][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.586][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.587][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:07.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:07.590][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.590][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-18 16:02:07.591][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:07.592][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.593][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.595][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:07.595][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:07.595][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:07.595][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:07.595][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:07.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:07.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:07.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:07.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:07.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:07.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:07.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.603][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.604][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:07.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:07.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.607][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.608][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-18 16:02:07.611][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.612][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:07.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.614][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:07.615][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.617][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.618][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.619][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.621][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:07.622][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:07.624][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.625][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-18 16:02:07.626][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:07.628][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.629][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.630][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:07.630][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:07.630][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:07.630][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:07.630][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:07.632][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:07.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:07.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:07.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:07.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:07.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:07.638][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.639][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.640][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:07.641][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:07.642][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.643][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.645][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-18 16:02:07.646][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.647][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-18 16:02:07.648][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.649][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:07.651][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.652][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.653][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.677][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.679][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:07.681][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:07.683][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.685][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-18 16:02:07.686][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:07.688][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.689][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.690][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.691][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:07.693][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:07.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:07.695][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:07.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:07.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:07.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.700][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.701][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:07.701][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:07.702][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.703][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.705][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-18 16:02:07.707][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.708][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:07.709][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.710][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:07.710][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.711][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.713][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.714][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.715][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:07.716][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:07.717][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.718][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-18 16:02:07.720][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:07.721][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.723][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:07.724][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.725][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:07.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:07.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:07.727][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:07.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:07.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:07.730][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:07.731][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.733][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:07.734][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:07.735][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:07.736][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:07.737][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:07.738][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.757][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[2025-10-18 16:02:07.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.824][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-18 16:02:07.826][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-18 16:02:07.828][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-18 16:02:07.829][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-18 16:02:07.831][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-18 16:02:07.833][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-18 16:02:07.834][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:07.835][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:07.837][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-18 16:02:07.838][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-18 16:02:07.839][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-18 16:02:07.840][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-18 16:02:07.842][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:07.843][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:07.845][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:07.846][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:07.848][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-18 16:02:07.849][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-18 16:02:07.850][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-18 16:02:07.852][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-18 16:02:07.853][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-18 16:02:07.854][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-18 16:02:07.855][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-18 16:02:07.856][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-18 16:02:07.857][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-18 16:02:07.859][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-18 16:02:07.860][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-18 16:02:07.861][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-18 16:02:07.862][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-18 16:02:07.863][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-18 16:02:07.865][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-18 16:02:07.866][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-18 16:02:07.867][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-18 16:02:07.868][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-18 16:02:07.869][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-18 16:02:07.870][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-18 16:02:07.871][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-18 16:02:07.873][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-18 16:02:07.874][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-18 16:02:07.875][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-18 16:02:07.876][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-18 16:02:07.877][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-18 16:02:07.878][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-18 16:02:07.879][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-18 16:02:07.881][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-18 16:02:07.882][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:07.883][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-18 16:02:07.884][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-18 16:02:07.885][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-18 16:02:07.886][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-18 16:02:07.888][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-18 16:02:07.889][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-18 16:02:07.894][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-18 16:02:07.895][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-18 16:02:07.897][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-18 16:02:07.898][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-18 16:02:07.899][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-18 16:02:07.900][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-18 16:02:07.901][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-18 16:02:07.902][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-18 16:02:07.903][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-18 16:02:07.904][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-18 16:02:07.905][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-18 16:02:07.906][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-18 16:02:07.907][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-18 16:02:07.909][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-18 16:02:07.910][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-18 16:02:07.911][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-18 16:02:07.912][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-18 16:02:07.913][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-18 16:02:07.914][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-18 16:02:07.915][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-18 16:02:07.916][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-18 16:02:07.917][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-18 16:02:07.918][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-18 16:02:07.919][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-18 16:02:07.920][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-18 16:02:07.921][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-18 16:02:07.922][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-18 16:02:07.924][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-18 16:02:07.925][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-18 16:02:07.926][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-18 16:02:07.927][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-18 16:02:07.928][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-18 16:02:07.929][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:07.930][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:07.931][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.932][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:07.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:07.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:07.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:07.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:07.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:07.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:07.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:08.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:08.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:08.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:08.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:08.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:08.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:08.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:08.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:08.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:08.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:08.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:08.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:08.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:08.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:08.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:08.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:08.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:08.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:08.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:08.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:08.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:08.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:08.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:08.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:08.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:08.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:08.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:08.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:08.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:08.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:08.023][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:08.031][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-18 16:02:08.033][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.033][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-18 16:02:08.034][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.035][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:08.036][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.037][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.037][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.038][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.039][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-18 16:02:08.040][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:08.041][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.042][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-18 16:02:08.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:08.043][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-18 16:02:08.043][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-18 16:02:08.044][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:08.045][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:08.046][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:08.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:08.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:08.048][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:08.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:08.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:08.050][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.050][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-18 16:02:08.050][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-18 16:02:08.051][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:08.052][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:08.053][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.057][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:08.059][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-18 16:02:08.060][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.061][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-18 16:02:08.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.063][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:08.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.064][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.065][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.066][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.066][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:08.067][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:08.068][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.069][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-18 16:02:08.069][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:08.070][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-18 16:02:08.070][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-18 16:02:08.070][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-18 16:02:08.070][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-18 16:02:08.070][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-18 16:02:08.070][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-18 16:02:08.071][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:08.072][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:08.072][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:08.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:08.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:08.074][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:08.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:08.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:08.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.078][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:08.078][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:08.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:08.079][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:08.080][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.081][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:08.081][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-18 16:02:08.083][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:08.084][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-18 16:02:08.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.085][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:08.086][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.087][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.088][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.089][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.089][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:08.090][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:08.091][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.092][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.093][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:08.094][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:08.095][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:08.095][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:08.095][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:08.096][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-18 16:02:08.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:08.097][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:08.098][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:08.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:08.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:08.100][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.101][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:08.101][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:08.101][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-18 16:02:08.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:08.102][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:08.103][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.104][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-18 16:02:08.105][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-18 16:02:08.106][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.107][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-18 16:02:08.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:08.109][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.110][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.111][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.112][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.112][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:08.113][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:08.114][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.115][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-18 16:02:08.116][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:08.116][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-18 16:02:08.116][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-18 16:02:08.117][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:08.118][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:08.119][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-18 16:02:08.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:08.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:08.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:08.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:08.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:08.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:08.124][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:08.124][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:08.124][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-18 16:02:08.125][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:08.125][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:08.126][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:08.127][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-18 16:02:08.128][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-18 16:02:08.129][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:08.130][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:08.131][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-18 16:02:08.132][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:08.138][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-18 16:02:08.144][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-18 16:02:08.151][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-10-18 16:02:08.154][biodb::testThat]
biodb.INFO [2025-10-18 16:02:08.155][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-18 16:02:08.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:08.156][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:08.158][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-10-18 16:02:08.159][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:02:08.162][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-10-18 16:02:08.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:02:08.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:08.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:08.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:08.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:08.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:08.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-18 16:02:08.174][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.175][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.177][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.190][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.191][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.192][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.197][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.198][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.199][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.200][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.203][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.204][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.206][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.207][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.210][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.211][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.212][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.213][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.216][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.217][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.219][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.225][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.228][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-18 16:02:08.229][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.231][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.232][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-18 16:02:08.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.235][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.236][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.237][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.241][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.242][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.244][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.248][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.248][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.250][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.254][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:08.255][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:08.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.256][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.258][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:08.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:08.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.261][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-18 16:02:08.262][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.264][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-18 16:02:08.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.268][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.269][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.271][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.272][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.275][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.276][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.278][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.282][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-10-18 16:02:08.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.285][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.291][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-10-18 16:02:08.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.294][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.297][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.305][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-10-18 16:02:08.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.314][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-10-18 16:02:08.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.317][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.320][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.324][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-10-18 16:02:08.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.330][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:08.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:08.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.336][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.346][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:08.369][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-10-18 16:02:08.371][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:08.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:08.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.374][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:08.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:08.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.377][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:08.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:08.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.384][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:08.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:08.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.387][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:08.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:08.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:08.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:08.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.394][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:08.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:08.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.436][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.439][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:08.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.459][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.460][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.462][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.478][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-18 16:02:08.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.488][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-18 16:02:08.489][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.490][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.491][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-18 16:02:08.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-18 16:02:08.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.511][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-18 16:02:08.512][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.513][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-18 16:02:08.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.533][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.534][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.535][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.550][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:08.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:08.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.553][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:08.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:08.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.556][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:08.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:08.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.559][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:08.560][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:08.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.562][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.562][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:08.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:08.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.572][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.576][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.579][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.582][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.582][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.584][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.585][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.595][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.601][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.605][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.605][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.607][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.624][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.632][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.632][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.634][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.645][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.648][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.651][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.655][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.656][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.657][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.658][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.668][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.679][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.679][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.681][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.692][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.698][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.701][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.701][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.703][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.704][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.722][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.728][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.729][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.730][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.731][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:08.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:08.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:08.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:08.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:08.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:08.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.753][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:08.753][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:08.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.755][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:08.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:08.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.776][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.777][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.778][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.804][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.804][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.806][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.817][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.818][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.820][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.824][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.825][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.827][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.831][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.832][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.834][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.838][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.839][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.841][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.845][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.846][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.848][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.853][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.854][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.855][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.860][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.860][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.862][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.866][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.868][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.869][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.874][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.874][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:08.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.876][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.880][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:08.881][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:08.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.887][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.892][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.893][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:08.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.894][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.899][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.900][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.901][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.906][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:08.906][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:08.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.908][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.912][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.913][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:08.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.914][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.919][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.920][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:08.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.922][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.926][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-10-18 16:02:08.928][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:02:08.929][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-10-18 16:02:08.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:02:08.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:08.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:08.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:08.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:08.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:08.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-18 16:02:08.940][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.941][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.943][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:08.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:08.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.947][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.948][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.949][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.950][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:08.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.953][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.954][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.956][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.957][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:08.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.960][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.960][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.962][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.963][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:08.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.966][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.967][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.972][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.973][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:08.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.976][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.977][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.978][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.979][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:08.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.982][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-18 16:02:08.983][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.984][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.986][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-18 16:02:08.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:08.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.989][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.989][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.991][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.992][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:08.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:08.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.995][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:08.996][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:08.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:08.998][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:08.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:09.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:09.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.002][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.003][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.005][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.009][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:09.010][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:09.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.012][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.013][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:09.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:09.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.016][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-18 16:02:09.017][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.019][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-18 16:02:09.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.023][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.024][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.025][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.030][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.031][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.032][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.036][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-10-18 16:02:09.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.040][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.051][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-10-18 16:02:09.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.057][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.060][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-10-18 16:02:09.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.070][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-10-18 16:02:09.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.073][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.079][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-10-18 16:02:09.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.092][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.095][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.101][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:09.129][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-10-18 16:02:09.130][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:09.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:09.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.134][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:09.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:09.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.137][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:09.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:09.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:09.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:09.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.143][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:09.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:09.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.147][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:09.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:09.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.150][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:09.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:09.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.162][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.190][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.193][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.196][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:09.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.219][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.220][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.222][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.243][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.246][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.268][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.269][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.271][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.282][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:09.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:09.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:09.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:09.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:09.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:09.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.297][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:09.298][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:09.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.300][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.300][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:09.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:09.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.311][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:09.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:09.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.315][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:09.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:09.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.318][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:09.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:09.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.321][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:09.322][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:09.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.324][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.325][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:09.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:09.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.339][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.345][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.346][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.348][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.349][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.359][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.363][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.366][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.370][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.370][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.372][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.373][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.397][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.398][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.400][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:09.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:09.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:09.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:09.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:09.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:09.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.420][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:09.421][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:09.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.422][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:09.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:09.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.433][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.443][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.444][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.445][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.446][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.471][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.478][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.479][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.480][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.481][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.501][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.502][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.503][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.504][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.525][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.526][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.527][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.546][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.550][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.550][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.557][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.558][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.579][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.581][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.593][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:09.594][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:09.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.596][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.600][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.601][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-18 16:02:09.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.602][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.607][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.608][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-18 16:02:09.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.610][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.614][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.615][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-18 16:02:09.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.617][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.622][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.623][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:09.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.624][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.629][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.630][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:09.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.631][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.636][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:09.637][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:09.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.638][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.643][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:09.649][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:09.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.651][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.656][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.656][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:09.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.658][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.663][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-18 16:02:09.664][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-18 16:02:09.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.665][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.670][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.671][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.672][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.677][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.678][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:09.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.679][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.683][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.684][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.686][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.691][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.692][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-18 16:02:09.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.693][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.698][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.698][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-18 16:02:09.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.700][ef$get] fields variable is a list.
biodb.INFO [2025-10-18 16:02:09.707][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.708][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-18 16:02:09.709][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.710][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:09.711][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-18 16:02:09.715][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-18 16:02:09.716][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:09.717][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:09.718][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:09.719][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:09.719][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:09.720][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-18 16:02:09.731][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.732][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-18 16:02:09.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.733][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:09.740][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.742][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.743][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:09.745][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-10-18 16:02:09.753][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-18 16:02:09.754][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:09.755][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:09.756][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:09.757][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:09.757][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:09.758][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:09.759][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:09.780][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.781][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-18 16:02:09.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.783][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:09.790][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-18 16:02:09.791][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:09.792][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:09.793][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:09.794][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:09.795][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:09.796][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:09.797][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:09.808][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.809][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-18 16:02:09.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.811][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:09.814][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-18 16:02:09.815][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:09.816][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:09.817][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:09.818][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:09.823][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:09.824][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:09.826][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:09.837][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.838][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-18 16:02:09.839][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.840][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.852][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.853][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-18 16:02:09.854][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.854][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.866][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.867][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:09.868][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.869][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.881][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.882][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:09.882][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.883][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:09.906][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:09.907][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:09.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.908][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:09.909][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.910][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:09.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:09.912][ef$get] fields variable is a list.
biodb.INFO [2025-10-18 16:02:09.913][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.914][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-10-18 16:02:09.915][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.916][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:09.922][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-18 16:02:09.923][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:09.924][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:09.925][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:09.926][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:09.927][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:09.928][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:09.929][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:09.941][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.942][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-10-18 16:02:09.943][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.943][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:09.946][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-18 16:02:09.947][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-18 16:02:09.948][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:09.949][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:09.950][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:09.951][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:09.951][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:09.952][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-18 16:02:09.964][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.965][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-10-18 16:02:09.966][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.967][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:09.969][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-18 16:02:09.970][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-18 16:02:09.971][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:09.972][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:09.973][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:09.974][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:09.975][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:09.976][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-18 16:02:09.992][biodb::testThat]
biodb.INFO [2025-10-18 16:02:09.993][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-10-18 16:02:09.994][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:09.995][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:09.998][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-18 16:02:09.999][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-18 16:02:10.000][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:10.001][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:10.002][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:10.002][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:10.003][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:10.004][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.TRACE[2025-10-18 16:02:10.016][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:10.017][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:10.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.019][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.019][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:10.020][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-18 16:02:10.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.022][ef$get] fields variable is a list.
biodb.INFO [2025-10-18 16:02:10.023][biodb::testThat]
biodb.INFO [2025-10-18 16:02:10.024][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-10-18 16:02:10.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:10.026][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:10.028][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-18 16:02:10.029][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-18 16:02:10.030][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:10.031][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:10.032][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:10.033][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:10.034][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:10.034][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-18 16:02:10.047][biodb::testThat]
biodb.INFO [2025-10-18 16:02:10.047][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-10-18 16:02:10.048][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:10.049][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:10.052][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-18 16:02:10.053][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-18 16:02:10.054][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:10.055][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:10.056][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:10.057][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:10.057][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:10.058][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-18 16:02:10.074][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-18 16:02:10.075][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-10-18 16:02:10.076][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-18 16:02:10.077][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.078][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.080][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-18 16:02:10.084][biodb::testContext]
biodb.INFO [2025-10-18 16:02:10.085][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:10.085][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-10-18 16:02:10.086][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:10.087][biodb::testContext]
biodb.INFO [2025-10-18 16:02:10.089][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:10.090][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:10.094][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:10.095][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-18 16:02:10.096][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-18 16:02:10.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.099][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-18 16:02:10.100][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-18 16:02:10.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.102][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-18 16:02:10.103][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-18 16:02:10.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.106][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-18 16:02:10.107][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-18 16:02:10.108][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-18 16:02:10.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.110][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-18 16:02:10.111][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-18 16:02:10.112][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-18 16:02:10.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.115][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-18 16:02:10.116][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-18 16:02:10.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.118][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-18 16:02:10.119][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-18 16:02:10.120][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-18 16:02:10.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.123][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-18 16:02:10.124][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-18 16:02:10.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.126][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-18 16:02:10.127][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-18 16:02:10.128][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-18 16:02:10.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.131][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:10.132][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-18 16:02:10.133][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-18 16:02:10.133][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-18 16:02:10.134][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-18 16:02:10.135][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-18 16:02:10.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.138][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-18 16:02:10.139][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-18 16:02:10.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.146][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-18 16:02:10.147][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-18 16:02:10.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.151][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-18 16:02:10.151][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-18 16:02:10.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.154][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-18 16:02:10.155][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-18 16:02:10.156][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-18 16:02:10.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.159][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:10.160][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-18 16:02:10.178][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-18 16:02:10.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.181][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-18 16:02:10.182][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-18 16:02:10.183][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-18 16:02:10.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.186][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-18 16:02:10.188][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.189][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-18 16:02:10.190][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.190][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:10.191][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.192][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.193][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.194][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.195][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:10.196][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:10.196][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.197][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-18 16:02:10.198][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:10.199][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.200][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.201][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:10.201][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:10.201][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:10.201][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:10.201][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:10.202][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:10.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:10.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.206][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.207][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.208][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:10.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:10.209][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.210][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.211][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-18 16:02:10.213][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.214][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:10.214][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.215][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:10.216][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.217][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.218][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.219][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.219][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:10.220][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:10.221][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.222][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-18 16:02:10.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:10.224][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.224][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.225][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:10.225][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:10.225][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:10.225][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:10.225][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:10.226][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:10.227][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.228][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.229][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:10.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.231][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.232][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.232][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:10.233][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:10.234][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.235][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.236][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-18 16:02:10.241][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.242][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-18 16:02:10.243][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.244][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:10.245][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.246][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.246][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.247][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.248][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:10.249][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:10.250][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.250][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-18 16:02:10.251][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:10.252][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.253][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.254][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.254][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:10.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.256][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:10.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.258][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.259][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.260][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:10.261][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:10.261][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.262][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.263][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-18 16:02:10.265][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.265][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:10.266][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.267][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:10.268][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.269][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.269][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.270][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.271][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:10.272][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:10.273][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.274][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-18 16:02:10.274][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:10.275][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.276][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.277][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.278][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:10.279][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.280][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:10.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.282][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.283][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.284][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:10.285][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:10.285][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.286][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.287][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:10.288][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.296][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[2025-10-18 16:02:10.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.308][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[2025-10-18 16:02:10.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.346][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[2025-10-18 16:02:10.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.354][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-18 16:02:10.355][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-18 16:02:10.356][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-18 16:02:10.357][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-18 16:02:10.358][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-18 16:02:10.359][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-18 16:02:10.361][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:10.362][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:10.363][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-18 16:02:10.364][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-18 16:02:10.365][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-18 16:02:10.366][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-18 16:02:10.367][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:10.368][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:10.369][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:10.371][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:10.372][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-18 16:02:10.373][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-18 16:02:10.374][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-18 16:02:10.375][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-18 16:02:10.376][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-18 16:02:10.378][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-18 16:02:10.379][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-18 16:02:10.380][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-18 16:02:10.381][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-18 16:02:10.382][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-18 16:02:10.384][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-18 16:02:10.385][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-18 16:02:10.386][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-18 16:02:10.387][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-18 16:02:10.393][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-18 16:02:10.394][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-18 16:02:10.395][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-18 16:02:10.397][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-18 16:02:10.398][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-18 16:02:10.399][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-18 16:02:10.400][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-18 16:02:10.401][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-18 16:02:10.402][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-18 16:02:10.403][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-18 16:02:10.405][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-18 16:02:10.406][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-18 16:02:10.407][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-18 16:02:10.408][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-18 16:02:10.409][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-18 16:02:10.410][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:10.412][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-18 16:02:10.413][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-18 16:02:10.414][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-18 16:02:10.415][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-18 16:02:10.416][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-18 16:02:10.417][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-18 16:02:10.419][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-18 16:02:10.420][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-18 16:02:10.421][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-18 16:02:10.422][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-18 16:02:10.423][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-18 16:02:10.425][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-18 16:02:10.426][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-18 16:02:10.427][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-18 16:02:10.428][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-18 16:02:10.429][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-18 16:02:10.430][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-18 16:02:10.431][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-18 16:02:10.432][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-18 16:02:10.434][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-18 16:02:10.435][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-18 16:02:10.436][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-18 16:02:10.437][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-18 16:02:10.438][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-18 16:02:10.439][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-18 16:02:10.440][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-18 16:02:10.442][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-18 16:02:10.443][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-18 16:02:10.444][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-18 16:02:10.445][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-18 16:02:10.446][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-18 16:02:10.447][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-18 16:02:10.448][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-18 16:02:10.450][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-18 16:02:10.451][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-18 16:02:10.452][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-18 16:02:10.453][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-18 16:02:10.454][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-18 16:02:10.456][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:10.457][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:10.457][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.459][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:10.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:10.686][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:10.694][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-18 16:02:10.695][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.696][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-18 16:02:10.697][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.698][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:10.698][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.699][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.700][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.700][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.701][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-18 16:02:10.702][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:10.703][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.703][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-18 16:02:10.704][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:10.705][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-18 16:02:10.705][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-18 16:02:10.706][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.706][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.707][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:10.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:10.710][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.711][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.712][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-18 16:02:10.712][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-18 16:02:10.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:10.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:10.714][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.715][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.716][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-18 16:02:10.717][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.718][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-18 16:02:10.719][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.719][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:10.720][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.721][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.722][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.723][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.723][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:10.724][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:10.725][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.726][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-18 16:02:10.726][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:10.727][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-18 16:02:10.727][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-18 16:02:10.727][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-18 16:02:10.727][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-18 16:02:10.727][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-18 16:02:10.727][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-18 16:02:10.728][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.728][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:10.729][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:10.730][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.731][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.731][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:10.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.734][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.734][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:10.734][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:10.735][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:10.736][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:10.737][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.737][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.738][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-18 16:02:10.740][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.740][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-18 16:02:10.741][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.742][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:10.743][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.743][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.744][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.745][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.746][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:10.746][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:10.747][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.748][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-18 16:02:10.748][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.749][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-18 16:02:10.750][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.751][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:10.751][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:10.751][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:10.752][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-18 16:02:10.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.754][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:10.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.756][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.757][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:10.757][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:10.757][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-18 16:02:10.758][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:10.758][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:10.759][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.760][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-18 16:02:10.761][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-18 16:02:10.762][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.763][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-18 16:02:10.764][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.765][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:10.766][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.767][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.769][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:10.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:10.771][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.772][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-18 16:02:10.773][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:10.774][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-18 16:02:10.774][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-18 16:02:10.775][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:10.775][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:10.776][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-18 16:02:10.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.779][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:10.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:10.780][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:10.781][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:10.782][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:10.782][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-18 16:02:10.782][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-18 16:02:10.783][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:10.784][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:10.785][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:10.786][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-18 16:02:10.787][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-18 16:02:10.788][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:10.789][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:10.790][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-18 16:02:10.792][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:10.793][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-18 16:02:10.797][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-18 16:02:10.804][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-10-18 16:02:10.808][biodb::testThat]
biodb.INFO [2025-10-18 16:02:10.809][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-18 16:02:10.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:10.811][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:10.813][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-10-18 16:02:10.814][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:02:10.817][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-10-18 16:02:10.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:02:10.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:10.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:10.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:10.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:10.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:10.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-18 16:02:10.830][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.831][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.833][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.848][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:10.849][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:10.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.850][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.851][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:10.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:10.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.855][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.858][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.865][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:10.889][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-10-18 16:02:10.891][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:10.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.894][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-18 16:02:10.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-18 16:02:10.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.898][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:10.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-18 16:02:10.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.902][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:10.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:10.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.905][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:10.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:10.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.909][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:10.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:10.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.913][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:10.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:10.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.924][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.954][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.958][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-18 16:02:10.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.984][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.985][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.987][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:10.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:10.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:10.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:10.998][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:10.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:11.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:11.001][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:11.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:11.004][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:11.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:11.008][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.009][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:11.010][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:11.011][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:11.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:11.021][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:11.022][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:11.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:11.024][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:11.028][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.029][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:11.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:11.031][ef$get] fields variable is a list.
biodb.INFO [2025-10-18 16:02:11.038][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.039][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-18 16:02:11.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:11.040][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:11.042][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-10-18 16:02:11.045][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:11.046][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:11.047][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:11.048][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:11.049][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:11.050][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:11.050][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:11.062][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.063][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-18 16:02:11.064][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:11.065][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.071][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.072][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-18 16:02:11.072][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:11.073][biodb::testThat]
biodb.WARN [2025-10-18 16:02:11.076][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-18 16:02:11.079][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-18 16:02:11.087][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.088][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-18 16:02:11.089][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:11.089][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:11.093][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-10-18 16:02:11.093][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-10-18 16:02:11.095][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-18 16:02:11.096][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-10-18 16:02:11.096][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-18 16:02:11.097][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-18 16:02:11.098][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-18 16:02:11.099][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-18 16:02:11.119][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.120][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-18 16:02:11.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:11.122][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.134][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.135][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-18 16:02:11.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:11.137][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.149][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.150][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:11.151][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:11.152][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.164][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.165][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:11.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:11.167][biodb::testThat]
biodb.INFO [2025-10-18 16:02:11.179][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-18 16:02:11.180][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-10-18 16:02:11.181][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-18 16:02:11.181][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:11.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:11.183][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:11.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:11.184][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:11.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$getEntryPageUrl(id)
 12.                     └─private$doGetEntryPageUrl(entry.id)
 13.                       └─base::vapply(id, fct, FUN.VALUE = "")
 14.                         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$getEntryPageUrl(id)
 14.                         └─private$doGetEntryPageUrl(entry.id)
 15.                           └─base::vapply(id, fct, FUN.VALUE = "")
 16.                             └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 15.                           └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 16.                             └─self$getEntryPageUrl(id)
 17.                               └─private$doGetEntryPageUrl(entry.id)
 18.                                 └─base::vapply(id, fct, FUN.VALUE = "")
 19.                                   └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)

[ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]
Error: Test failures
In addition: Warning message:
In fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.13.1’
* 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 ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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’ ... WARNING
'library' or 'require' call not declared from: ‘biodbNci’
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]
  Error: Test failures
  In addition: Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log’
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.13.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)